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It's perfectly safe, and dare I say even something you probably should do, at least if you reuse projects and get a lot of items that have the same project name at the end.
I can't remember if it's buy/build or CAS files where you'll want to avoid extra punctuation marks in the files (they won't show up ingame) - but either way if you want to share files at some point, a lot of people tend to appreciate if you avoid special characters in filenames, so it can be a good habit to avoid those (letters A-Z without accent marks is fine, numbers are fine, _ is fine, - is usually fine. Avoid spaces and special characters, and keep names short but descriptive - "blue.package" is going to be very annoying when you have no clue what it is). There's a bit of debate on whether this naming system has an advantage on game loading (some say yes, others say no), but I have seen issues with extra punctuation marks where the game didn't read the files, plus accent marks where the uploading site couldn't handle the download without renaming the file, plus a few other issues related to file naming, so I say it's better safe than sorry. The cleaner the filenames are, the less likely any issues will happen.
I'm a bit unsure if sim files will work properly when renamed (honestly haven't tried much, but I think they will). They're the files with 8 random digits, then a _ , then 8 more digits. Personally I tend to leave these as-is, because I often have the sims packaged up elsewhere with that file in an un-renamed variant, and I don't want to have doubles with different names.
I also tend to move renamed files over to the Downloads folder (yes, you can do that - they work fine in there).