It isn’t clear whether you have legally merged yet or not.  You say you are in the process of merging, have merged, and ask about if you merge.  You obviously don’t want to merge your bank accounts until the merger has actually taken place and all the documents effecting the merger have been properly filed.

Assuming that you have legally completed a true merger — where one organization merges into the other and the survivor has all of the assets and liabilities of the other — you can merge the bank accounts, or not, any time you want.  Your administration of the surviving corporation is independent of its tax status.  The primary reason you might want to keep the accounts separate could be to make it easier to divide the surviving entity back into the original two if you don’t achieve the tax status you are seeking.  If you think re-division is a possibility, you will want to determine how to allocate receipts and expenses between the two accounts, whether you keep them separate or merge them now.  If you think there is no possibility of going backward, you probably don’t need these separate accounts or allocations.