Personally I would not recommend leaving deprecated prefabs in your project. If you're not careful, those deprecated files are extremely confusing for new team members, or when doing maintenance years down the road when you no longer remember every little detail. It also makes searching your project more tedious since your search results will include deprecated files.
I'd suggest either deleting the bad prefab, or just modifying to fix it rather than making a new version. If you ever need the old version again (why would you?) - that's what version control is for.
If you absolutely must keep the old prefab for some really legitimate reason and not out of a fear of ever deleting anything, you should rename it and include the word "Deprecated" in the new name.