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extracting tables and remapping headers

Apologies if this question is in the wrong category.  I'm unsure as to what's possible with FineReader vs Flexicapture, but here's my question...
I have several hundred pdfs that contain tables of data (+other image and text info).   Within the batch of docs, there are several variants on the table header naming convention.  For instance, some PDFs have a table with a column named 'Item' and another has a column named 'Position'.  I want to batch execute the extraction of the tables into a single CSV, combining certain columns into a single column (unifying the header name).  In addition, some of the PDFs have a text layer and some don't, but the goal is to extract the tables from all pdfs in an automated way (including ocr where needed).   Thanks in advance for any suggestions that the community can lend.  

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