1.) The scrape function is a great thing and looks very nice, but it also takes up a lot of space on the memory card. The "Remove" function does not remove the downloaded data, as initially assumed, but the entire ROM. How is it possible to completely delete the data from the scrape function instead of the entire ROM file? Where is all the data for this stored and is it easy to safely remove with a file manager?
The scraped data is not erased. Could be an interesting addition.
Depending on how you did the scraping (which program you used for scraping and options chosen), the scraped data is either in $HOME/.emulationstation/downloaded_images or in the Roms folder. See the docs.
2.) Can deleted modules or systems also be safely deleted from the "opt/retropie/emulators" folder as well as "opt/retropie/libretocores" and "opt/retropie/configs" without Retropie getting into problems?
When you uninstall an emulator/port, its installed data should be also deleted from /opt/retropie/emulators, /opt/retropie/libretrocores, /opt/retropie/ports. You don't need to delete it manually.
3.) When removing the ports, are the corresponding program folders or installations also completely removed, e.g. with "Kodi"? The corresponding folder in "ports" apparently only shows a configuration file, but not the entire program folder. I would like to check this and delete it myself if Retropie doesn't do this after removing the port from the configuration menu, especially since I don't know if I want to keep the player yet.
Just as with other installed emulator, user data from the ROMs folder is not deleted when uninstalling it. There may be folders left, created by the emulator/port, those you can delete manually if you wish.
4.) Can I simply back up the configuration including all emulators, cores and other folders (approx. 700 MB) from the "opt/retropie" directory 1:1 with Midnight Commander onto my external exFAT formatted SD card and, if necessary, simply copy it back under the shell or the pixel file manager in case an update broke something or all my settings were lost due to an update? The latter is particularly important to me.
I was able to copy the data. The only question is whether all the file permissions were copied or whether they are important at all with Retropie and have a negative effect in some way.
I've answered to this question in your other topic, I'm not going to repeat it here.
5.) Where can I find all the update and menu scripts that are responsible for the settings of Retropie, Emulation Station and RetroArch? Or are they also in the "opt/retropie" folder? I want to save that too. And are there any other folders belonging to Retropie outside of the "opt" directory?
The installation folder holds most of the TUI menus used for configurations - that's $HOME/RetroPie-Setup, which is a clone/copy of https://github.com/RetroPie/RetroPie-Setup. Not necessarily needed for a backup, since this is present already in an RetroPie image or can be easily added.
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Or I use this tutorial: https://www.makeuseof.com/tag/install-retropie-app-raspberry-pi/
I'd advise on using the RetroPie Docs, 3rd party sites may contain outdated information or simply dubious advices on how to install and 'optimize' RetroPie.
Also, I'm a bit confused about how to use Retroarch. After starting, I initially had a green menu and was able to conveniently save and load save states from the SNES9x with the controller by pressing the home button and one of the shoulder buttons on the controller at the same time. The remaining buttons were assigned the same way as you are used to from the SNES controller and as I had set it in Retropie in the controller menu. After updating Retroarch to the latest version,...
Not sure how you 'updated' RetroArch - updating the RetroPie package does not modify any user made configuration. It looks to me you've used the advanced menu in RetroArch and you used the Online Updater to update the controller profiles (probably among other things ?), ovewriting the RetroPie-generated profile for your controller. You don't need to 'update' RetroArch this way - the only downloadable update that's recommended is the Cheats database, not installed by RetroPie automatically.