Hopefully this is the right place for this. I originally tried posting it to the LibreOffice section of Bugzilla, but they sent me here instead.
I had LibreOffice 5.4.5 installed on my Win7 (x64) PC. My wife wanted a portable version on a USB stick. So I downloaded the portable version 6.0(.2?) and set it up on her stick. Now, the LibreOffice install on my PC doesn't work. It is still in my Start menu, but the shortcuts are pointing to drive F instead of E, where my install was. The uninstaller doesn't remove these traces, because it also wants to go to drive F. Likewise, attempting a new install won't run because it cannot find drive F either.
Eventually I solved the removal problem by inserting a random USB stick to take the drive F designation, ran the (standard Windows) installer for 6.0.2.1, and chose remove. I then used the same installer to reinstall LibreOffice.
It is counter-intuitive to me that putting a portable version on a stick would wipe out the preexisting install. Why assume the stick is intended to run on this PC? The installer should have asked before removing the old one from my hard drive. It would also be helpful if the installer would give you an opportunity to remove a borked install when it can't find a removable drive that it expects would hold much of the data it is looking for, perhaps offering a troubleshooting option rather than forcing a quit. After all, the drive may have been lost.
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Are you completey shure you used the portable version (named LibreOfficePortable_*.paf.exe)? It cannot not leave or alter any entries in the Start menu (because it has not real installer that interacts with windows itself but only copies files to a specific install position on the stick or any suitable folder) - that means it does not get "installed" in windows and therefore should not interfere with any local install nor leave any registration in programs etc. Windows does not even recognize its existence until you do some file associations or comparable. I (and many other users) have used both versions alongside many times without a problem. The symptoms, you describe point to the possibility, that you by mistake did a local install on your USB-drive (and that would definitely mess up an existing local install). Just a guess, but could you please check your downloaded portable file or report the exact way you downloaded the portable version? Is it from the app section here on PortableApps.com or directly from LibreOffice.org? I just checked and it seems, the downloads there are correct portable versions in paf-format.
I can't recreate the above issue. I installed LibreOffice 5.4.5 within a Windows 7 virtual machine, ran it to ensure it worked, installed LibreOffice Portable 6.0.2 in another location, LibreOffice 5.4.5 still worked without issue and the shortcuts all worked, ran LibreOffice Portable 6.0.2 and then closed it, LibreOffice 5.4.5 still worked without issue and the shortcuts all worked.
The LibreOfficePortable_6.0.2_MultilingualX.paf.exe installer has no code within it to do any local shortcuts or alter any local shortcuts. The only way the local shortcuts might change is if LibreOffice itself added code to take them over which I'm not aware of them doing and could not recreate in the above scenario.
Sometimes, the impossible can become possible, if you're awesome!