Mail Merge Problems with Converted PDFs

We have been doing mail merges for years with PDF forms that we convert to word.  However in the last couple of years we have noticed whenever we merge more than one document at once the number continues on the form onto the next document and overall the formatting is very off. This forces us to merge the documents one at a time instead of in batches.  I have tried flatting the document in adobe before converting but the issue still exists.  Anyone have any suggestions?