Unless you are using an older hash function that doesn't have sufficient collision or preimage resistance, that should not be an issue, because finding 2 files

Unless you are using an older hash function that doesn't have sufficient collision or preimage resistance, that should not be an issue, because finding 2 files that hash to the same output is infeasible. It does point to the need to be able to upgrade the hash function in your protocol at some point, and preferably associate a set of hashes generated by different hash functions to the same file contents.