I am starting to understand what you mean. What you call the Sosa Number is what is called in English an Ahnentafel Number. (It is the same exact numbering system, but for some reason we use a German name for it.)
By database I mean a genealogy file. In English, PAF database files have names ending in .paf(Database = base de donnees - Je ne veux pas dire le logiciel, mais les donnees dans le fichier.)
I doubt that the Custom ID numbers are causing any problem. PAF doesn't seem to care what is used for this purpose.