Most likely the 2 are not related. It's very difficult to diagnose this kind of stuff without seeing it....in general my personal feeling is to not touch the tables directly unless you are 100% sure of what you are doing. And no matter what, make backups before any changes!
For the batch issue, get everyone out of GP, make a backup of your DYNAMICS and company databases, then check the following tables, they should all be empty:
DYNAMICS..ACTIVITY
DYNAMICS..SY00800
DYNAMICS..SY00801
tempdb..DEX_LOCK
tempdb..DEX_SESSION
If everyone is out of GP, you can delete anything in those tables. If you're not sure, tell us what you see and we will help you figure out what it means.
Then take a look at SY00500 in the company database. Find the batch in question - ERRSTATE and BCHSTTUS should both be 0. If they are not, change them to 0, then in GP go the the Batch Entry window (Transactions > Financial > Batches), bring up that batch and print the Edit list (click the print icon in the upper right hand corner). That report should tell you if there will be a problem posting the batch. If there are no errors listed, post the batch again.
Again, I do not think the reconciliation issue is related, and if you've checked the CM20200 table and everything looks correct, then you may want to get some help with that from either your GP Partner or Dynamics GP support.
Victoria Yudin
Dynamics GP MVP
Flexible Solutions - home of GP Reports