I have been living the same nightmare here.
This method was popular when the CAD tools did not utilize a pdm program to manage data. There were no common file storage areas (each assy and its components resided in a single folder). Also, the CAD tool really had no means to efficiently export a parts list, so there was no benefit to proper file naming. Users would name the parts whatever helped them navigate the assembly. Unfortunately, the problem arose when it was time to move this legacy data into a pdm tool. The files needed to have unique p/n's. Still, many CAD tools had not yet adopted the use of attributes and parameters useful to navigate assemblies efficiently. Users just appended a unique number to their custom file name (ex: front_panel_123456.prt or johns_cover_123456.prt).
Some prefer to use non-intelligent part numbers (123456-1.prt), but I prefer the use of a commodity prefix (10-123456-1.prt). The prefix can be useful for downstream legacy applications which have sorting capabilities. The prefix would identify something like a purchased electrical component, a machined part, a sheetmetal part, an assembly, a special tool used, etc.
I have used many different part numbering systems, so if you have any questions just ask.
Thx, Mike