I’ve encountered these problems in projects with no version control as well, so I don’t think that’s it.
It does feel like I’m getting fewer crashes when I don’t use version control though.
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Try fixing up your redirectors: Asset Redirectors in Unreal Engine | Unreal Engine 5.1 Documentation
If you do not this can cause file folders to still appear or the naming issues you’ve pointed out.
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In addition to what flip hazard said, I oftentimes find myself with broken redirectors. They don’t show up as assets or redirectors in the engine and fixing redirectors doesn’t do anything. All I can do is delete the files via the explorer manually. In other words, the whole redirection system seems to be a bit unstable. It would be interesting to know how the teams at Epic are handling file management and whether there are any plans to fix it.