Can I merge two checking accounts used concurrently for several months? If yes, how?

Short answer is NO.   You should never merge two different Bank accounts with Individual Acct#, that will really mess up your tax records.

What report are you trying to run and what appears to be wrong with it?  Give us a few more details and hopefully someone here will have an answer.

And have you asked your Tax Accountant about whatever you think the issue is?  That's really were you're going to get the best answer on your Taxes.  Here you can get info on how to correct or change things in QBs, but none of us know your Company or under what Tax Rules you are filing.