Reflecting upon signs in the universe and Islamic teachings mentioned in the texts is one of the great acts of worship enjoined and encouraged in the Qur’an.
Allah, may He be exalted, says (interpretation of the meaning):
“Those who remember Allah (always, and in prayers) standing, sitting, and lying down on their sides, and think deeply about the creation of the heavens and the earth, (saying): Our Lord! You have not created (all) this without purpose, glory to You! (Exalted are You above all that they associate with You as partners). Give us salvation from the torment of the Fire”
[Aal ‘Imraan 3:191]
“Allah is He Who raised the heavens without any pillars that you can see. Then, He rose above (Istawâ) the Throne (in a manner that suits His Majesty). He has subjected the sun and the moon (to continue going round), each running (its course) for a term appointed. He manages and regulates all affairs, He explains the Ayât (proofs, evidences, verses, lessons, signs, revelations, etc.) in detail, that you may believe with certainty in the meeting with your Lord.
And it is He Who spread out the earth, and placed therein firm mountains and rivers and of every kind of fruits He made Zawjain Ithnaîn (two in pairs - may mean two kinds or it may mean: of two varieties, e.g. black and white, sweet and sour, small and big) He brings the night as a cover over the day. Verily, in these things, there are Ayât (proofs, evidences, lessons, signs, etc.) for people who reflect”
[ar-Ra‘d 13:2-3]
“Allah it is He Who has subjected to you the sea, that ships may sail through it by His Command, and that you may seek of His Bounty, and that you may be thankful,
And has subjected to you all that is in the heavens and all that is in the earth; it is all as a favour and kindness from Him. Verily, in it are signs for a people who think deeply”
[al-Jaathiyah 45:12-13].
This refers to reflecting upon the signs in the universe such as the heavens, the earth, mountains and rivers; that also includes reflecting upon one’s own self and how one was formed and created, as Allah, may He be glorified, says (interpretation of the meaning):
“And on the earth are signs for those who have Faith with certainty,
And also in your own selves. Will you not then see?”
[adh-Dhaariyaat 51:20-21].
With regard to reflecting upon Islamic teachings mentioned in the texts, Allah, may He be exalted, says (interpretation of the meaning):
“(This is) a Book (the Qur’an) which We have sent down to you, full of blessings that they may ponder over its Verses, and that men of understanding may remember”
[Saad 38:29].
Part of reflecting and pondering is looking at what one has sent on ahead of deeds.
The Qur’an teaches us to do that in the verse where it says (interpretation of the meaning):
“O you who believe! Fear Allah and keep your duty to Him. And let every person look to what he has sent forth for tomorrow, and fear Allah. Verily, Allah is All-Aware of what you do”
[al-Hashr 59:18].
This is taking stock of oneself. There is a famous report from ‘Umar (may Allah be pleased with him) that speaks of it:
Take stock of yourselves before you are brought to account; weigh yourselves before you are weighed, for that will make the Reckoning easier for you tomorrow, if you take stock of yourselves today and prepare yourselves for the great presentation on the Day when you will be be brought to Judgement, and not a secret of yours will be hidden.
Narrated by Ibn Abi’d-Dunya in Muhaasabat an-Nafs (p. 22); Ahmad in az-Zuhd (p. 120); Abu Nu‘aym in al-Hilyah (1/52). It was classed as da‘eef by al-Albaani in ad-Da‘eefah (1201) and by Abu Ishaaq al-Huwayni in his Takhreej li Tafseer Ibn Katheer (1/478). He said: The men of its isnaad are thiqaat (trustworthy) but there is a break in the chain between Thaabit ibn al-Hajjaaj and ‘Umar ibn al-Khattaab, because he never met him. End quote.
Taking stock of oneself is required before doing any deed, whilst doing it and after doing it, at all times.
Ibn Qudaamah (may Allah have mercy on him) said:
With regard to taking stock of oneself after the deed is done, Allah, may He be exalted, says (interpretation of the meaning):
“O you who believe! Fear Allah and keep your duty to Him. And let every person look to what he has sent forth for tomorrow”
[al-Hashr 59:18].
This refers to taking stock of oneself after doing any deed. Therefore ‘Umar (may Allah be pleased with him) said: Take stock of yourselves before you are brought to account.
Al-Hasan said: The believer is responsible for himself and must take stock of himself. And he said: The believer may see something (of worldly matters) by accident and like it, so he says: By Allah I desire you and you are something that I need, but by Allah I do not have the means to attain you; there is no way, for there is a barrier between me and you. And he may do something without thinking, so he starts checking himself, saying: Why did I do or say that? By Allah I will never go back to that again, if Allah wills.
The believers are people who are restrained by the Qur’an, which protects them and prevents them from indulging in that which could bring about their doom. The believer is a prisoner in this world, striving to ransom himself (from Hell), and nothing will make him feel secure until he meets Allah, may He be glorified and exalted. He knows that he will be brought to account for his hearing, his sight, his tongue and his physical faculties; he will be brought to account for all of that.
So it should be understood that just as the individual should have a time at the beginning of the day when he pledges to restrain himself and to do righteous deeds, he should also have a time at the end of the day when he examines himself and takes stock of himself and all that he did, just as traders in this world do with their partners at the end of every year or month or day. What is meant by taking stock is that he should look at his capital and his profits and losses, so that he may see whether he is gaining or losing. In religious terms, his capital is the obligatory duties; his profit is supererogatory deeds; and his loss is sin. So let him take stock, first of all, of obligatory duties, and if he commits a sin, let him impose on himself some sort of punishment, so as to make up for his heedlessness.
It was said that Tawbah ibn as-Summah was in ar-Raqqah, and he used to take stock of himself. One day when he was doing that, he realised that he was sixty years old. He worked out the number of days of his life, and realised that it was twenty-one thousand and five hundred days. He screamed and said: Woe is me! Am I going to meet the Sovereign with twenty-one thousand and five hundred sins? How about if there were ten thousand sins every day?! Then he fell down dead, and they heard a voice saying: How quickly he was taken to al-Firdaws al-A‘la (the highest Paradise)!
This is how a person should take stock of himself with every breath he takes, with every sin of the heart (i.e., thoughts, feelings and emotions) and every action he does, at every moment. If a man were to throw a stone into his house for every sin he commits, his house would be filled within a very short period of time. But he does not pay much attention to remembering his sins, although they have already been recorded against him. “Allah has kept account of it, while they have forgotten it” [al-Mujaadilah 58:6].
End quote from Mukhtasar Minhaaj al-Qaasideen (p. 373)
Thus you will realise that what you are doing of reflecting upon what you have committed of sins and what you have sent forth of good deeds, and what you have resolved to do in the future, is all something praiseworthy and required, and it comes under the heading of pondering, reflecting and taking stock. It is not an innovation (bid‘ah), and it does not matter whether the Sufis or anyone else does that.
What matters is that pondering and reflecting leads one to focus more on obedience to Allah and doing good deeds, and does not lead to despair and loss of hope.
But you should understand that repentance, reflection and checking and taking stock of oneself does not require special rituals, breathing exercises or special programs, and does not need to be done at any specific time of the night or day. Rather whenever it is possible for a person to be alone with his Lord, focus his mind on Him and converse with Him, that is the time for such acts of worship.
If there is any time that is preferred for that, then it is something that is to be learned from the Lawgiver, such as the latter part of the night and so on.
And Allah knows best.