So whats the best way to keep a clean file system, but not be subject to data corruption
As I understand it, You want to move unused files which may be needed later on.
I don't know of current open source software, but, assuming you are on Windows, winrar will do what you want. The trial version is not time limited. There might be open source software that does the same, but I don't have that at hand.
The problem you mentioned does apply to simple yip archives. They are dead when corrupted. Winrar on the other hand usually lets you get the rest of the files - don't click on solid archive because that would deactivate this capability.
Also you can specify up to 10% parity information, so up to 10% of the archive may be corrupted and it still can be reconstructed. Lastly winrar supports split archives with recovery volumes, which means that you can create additional part files that are just for data recovery if you lose one of the part files.
Under those circumstances I switched to archiving because it is safer than not archiving.
If you need input on other measures like RAID, *nix solutions like RAID, special filesystems like ZFS, just comment back and I will provide info to my best knowledge.
Sorry for the typos, I'm on a machine with wrong codepage.