if the files are local then as long as the full file path that's being reported back to wacup & the folder monitor hasn't changed then there duplicates shouldn't be added. yes there's been some builds which broken that but that's been resolved for some time (excluding the noted network path problem)

getting a copy of the "bad" local library db files with the duplicates showing would have been useful but as it seems you've started over again with the local library db they're gone. if it happens again then I'd need to get a copy of the library.dat/library.idx files from the wacup settings folder.