Balancing Subledger to GL after running Undo Accounting Script

We have had to run a couple different scripts where "undo accounting" has been run. I'm wondering what other people do to balance their subledger and the GL after running these scripts. If the transactions we are fixing is from a prior period my trial balance and subledger never balance. We are now in a situation where we are going to have to run this again and I don't want to keep doing this without a good way to balance to the GL each month. Any tips or recommendations would be appreciated.