Hi, Angelo,
I'm not familiar with the Bottomline program. If you have access to your "problem" data files, you can clone them with either the Maintenance Utility, or our Command Line Butil utility. Then, you should be able to copy the data in the problem files to the empty clones of those two files. At that point, you should replace the problem files with the freshly created and loaded copies.
If you are unable to implement the clone/copy suggestion, above, it may be time to contact the Bottomline folks.
Regards, shyde