I am not familiar with any specifics relating to bankruptcy but I have split companies when they changed from S-Corp to LLC or some such and the premise is presumably the same.  A new company is created that is a copy of the existing company as of the startup or changeover date, then the GL is cleared so new beginning balances can be entered.  Sounds like that is what you did which is fine.
 
If you want to beging reconciling subledgers to the GL before you have the final beginning balance numbers as of the change date, you could make a GJ as of that date posting the accounts you know (typically AR, AP, Cash, possibly Inventory & WIP & RNI) and posting the other side to some temporary suspense account.  Then, when you have the full balanced entry for the startup, enter the rest of it and it should offset what is in the suspense account.
 
To reconcile the checking account, you can manually enter the correct beginning balance into AD-B for the first reconciliation (which will be a split between the 2 companies assuming that you are still using the same bank account.)