I've recently gotten used to deleting unused files with the "Clean project directory" function without any worry at all anymore. In the early days I was still unclear as to how Reaper handled files and X'ed off a few files that I shouldn't have. Like drum loops that I put into a project that were also in other projects. Not to mention the loops folder. The solution?
Always, always "Save as" for one. The first time around make sure you "Create subdirectory project". You obviously don't need to do this more than once. However; if you are adding, not recording, wave files of any kind into a project the key is to:
"Copy all media into project directory".
Do this every time you bring in a new file. This way you don't disrupt, move, alter, or change the source files which will be nice when you try to use them again in the future and they're still there! And you can butcher to your hearts content!
This is especially useful when slicing and dicing loops for use in the project at hand. The scraps tend to be named the same as the files staying in the project but reaper knows what you've stopped using, so when you X it off you know your chucking waste. This has really helped to keep the project folder free from confusing clutter. And since doing things this way I have not lost anything I didn't want to.