Is repentance from sins that cause one to abandon their religion valid and acceptable, even without certainty that these sins were committed, and is this repentance sufficient to forgive the sin if it is later confirmed?

Repentance is a good deed that is commanded. If you make a general repentance, it will benefit you and erase your sins. What you intend to do to get rid of the whispers is fine, although the original premise is that you have not committed anything that necessitates apostasy. Therefore, you should not pay attention to these whispers, for they are from the cunning of Satan.