I'm currently cleaning up the entries that are >90 days AP, trying to match up entries to clear them out. Am I able to do so without effecting previous reconciliations?

It really depends how transactions were entered.

Lets say you have a bill from Feb 2021 outstanding. If it has been paid, how was payment entered? Did they create a new bill or it was entered as an expense?

Without looking at each transaction, it will be hard to give an accurate answer. I suggest to use the "Find a proadvisor" service and work with a QBO proadvisor.

Hi there lex-barber-fansu,

It's vital that all the transactions are correctly entered in your books so that the accounts will be balanced. QuickBooks Online's reconcile feature is there to make sure that your bank has all the necessary transactions for the bank balance to represent reality. I can point you in the right direction for assistance with the transactions.

As stated by Prachijoshi, an analysis of each transaction would be needed to see how deleting the transaction would affect the bank reconcile and your accounting overall. I recommend reaching out to your accountant in order to see if those transactions are correctly entered and the best way to correct them if they aren't. You can add them to your account by navigating to the My accountant tab. You can also find an accountant near you by clicking the Find a pro to help button.

If you have any other questions, feel free to reach out here.

@lex-barber-fansu 

If you need to self clean your account up, utilize the trial version of a backup restore app.

https://rewindio.grsm.io/quickbooks