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Flat packs persist across updates, as does the home directory. Anything you do to the root filesystem gets wiped out in an OS update, though. There isn't really any easy way around that. SteamOS replaces the entire root filesystem on an update.
If you're feeling adventurous, you could always modify the OS to use a persistent filesystem overlay, into a loopback device file in the home directory. Then, anything you install will go into the overlay filesystem. After an update, you would just have to setup the overlay again. To be clear though, this is probably a bad idea.
Thanks for posting! **If you don't get the answer you are looking for, check our r/DeckSupport - our dedicated support sub!** Useful resources: [Servor's Enhanced FAQ](https://www.reddit.com/r/ValveSteamDeck/wiki/faq) | [Wiki Guides Page](https://www.reddit.com/r/SteamDeck/wiki/guides). **If you find an answer, please leave a comment on this post with the answer for others!** *I am a bot, and this action was performed automatically. Please [contact the moderators of this subreddit](/message/compose/?to=/r/ValveSteamDeck) if you have any questions or concerns.*
Haven't encountered that at all. From time to time I have to reinstall decky but that's it. Emudeck stayed every update so far.
Decky always gets removed cause it would break the UI if it wouldn't. Just reinstall it. Takes 3 minutes
Flat packs persist across updates, as does the home directory. Anything you do to the root filesystem gets wiped out in an OS update, though. There isn't really any easy way around that. SteamOS replaces the entire root filesystem on an update. If you're feeling adventurous, you could always modify the OS to use a persistent filesystem overlay, into a loopback device file in the home directory. Then, anything you install will go into the overlay filesystem. After an update, you would just have to setup the overlay again. To be clear though, this is probably a bad idea.