There are several ways to copy protect software in unix.
One is to use a file that contains the inode number of that file, so that when the entire product is copied to another machine the probability of that file having the same inode number is miniscule.
Another is to use a sparse file. This is a file purposely fragmented (to use Microsoft words) when it is created. If this file is copied to another location, the 'gap' disappears and the file becomes contiguous.

However, after re-reading your original post, I think that copy protection is probably not the case, but rather that because you ran out of disk space, the data files are out of sync.
What I mean by that is Pro5 uses ISAM files that are made up of a data file, and a separate index file (eg CUST.DAT and CUST.IDX). There should be a utility that will allow you to rebuild corrupted databases, so that, in the example above, CUST.IDX is forced to reflect the data that is found in CUST.DAT
Sorry to sound so vague about the rebuild, but I haven't used this software for at least 5 years, and we just moved, and and the documentation is somewhere deep in a 48 foot trailer.

Jack