I have been using Libre in safe mode for a couple of months because I couldn’t open it after a Windows update. What do I need to do to get back to normal operations? Will I lose the files before or after working in Safe Mode?
If you have to ask this, I strongly advise to check your backup strategy. If you have external copies of your files you can not loose them by any updates, crashes etc. So this is generally advised.
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The other point Al has already answered: As Safe-mode means only ignore the current profile, it has nothing to do with your saved document unless you purposefully searched for the profile and saved documents inside. - Not impossible, but very unlikely.
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Further to @Wanderer comment, this page might be useful, Preventing data disaster - The Document Foundation Wiki
It was a Windows Update, let’s suppose that LibreOffice was open at the time it forced a restart. That might have corrupted the user profile because LO was not able to write back to it in an orderly manner as it was forced to shut. There are two ways to reset a user profile, I prefer the manual procedure because it is easier to copy back files that you might need, LibreOffice user profile - The Document Foundation Wiki
It might be a graphics issue but the hardware hasn’t changed so unlikely.
No, assuming you store them in Documents or somewhere sensible.
There is a proviso, Templates, macros, user dictionaries, etc. as listed in link above can be lost but because you have been using safe mode for a couple of months and you start with a fresh user profile each time, you wouldn’t notice. If you copy back the contents of those folders from your original user profile then you will get back some of your customisations that you had two months ago.