The best way to migrate your old modified files to the new patch format is to export your modified file as a TSV file, then export the unmodified 1.2 patch.pack file to a TSV file with another name, open both in a spreadsheet editor and create the new columns as needed (compare the files) - save it over the patched TSV. Also make sure that the version line (second line in the TSV file) shows "1.2".
Then import your modified TSV file again using the import TSV option. Now all your changes should appear.

Please note that PFM 1.11b TSV import/export mechanism is not compatible to previous version so you have to re-export any TSV files you're using.