This is an attempt by DIM to play nice if you use it to install in a directory with manually installed content.
The main issue is not the install - it is when you come along later and un-install something. DIM will delete everything that was in that package. BUT - there are some packages that share an item. For example, most of Jepe’s effectZ use the same .obj and un-installing one will delete the .obj and cause the others to fail. DIM creates a ‘registry’ in a folder by scanning all files and noting the number of times a file is referenced. Then, when you delete something, it decrements the count in the registry and will remove items with a zero reference count.
The ‘Fix’ option re-runs the scan and updates the current count. As near as I can tell. Probably not an issue if you don’t mix manual and DIM installs or if you don’t un-install products.