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I just tried to duplicate your problem using my copy of PAF 5.2.18 and it didn't happen. I firstly checked my PAF file with Check/Repair, which found no errors.
I exported everything to a gedcom file, created a new PAF file and then imported the gedcom into it. The Custom IDs were still in their own field, unchanged.
I added Custom ID to to the Individual screen to make it easy to check them. (Right-clicked the column headings and added Custom ID.)
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