Sorry for the late response. April 30 and May 1 are days off in Ukraine, and we were unable to answer you in these days.
Our implementation of a replication package with incremental updates requires LastModifiedDate and CreatedDate fields to be replicated. And after changes that we made for your packages, they require target to have the SystemModStamp column. We have already written to you that this is the reason we don't want to just switch from LastModifiedDate to SystemModStamp, and we decided to make it optional.
This case has two possible solutions:
1. We can rollback changes to your packages, and they will use LastModifiedDate again.
2. You can reset LastSyncTime for each package. Then select SystemModStamp for each object in each package. Then select the "Drop Tables" option, to recreate target tables and run your packages. As the result, the tables will be re-created with the SystemModStamp column. These packages will check whether a record changed, using the SystemModStamp column. All your packages will be restarted, and process all the records. We will reset your record counter for your account after this, so you won't need to pay for additional records in this case.
Please tell us, which option you select.