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I'm a huge fan of making custom controller tweaks and I too ran into [incompatible config] as often as Hello Games pushed the major version changes.
That led to the circle jerk, crab game of going into https://ibb.co/gzkk0S0
To delete all incompatible configs and exiting "Edit Layout via Steam" mini app.
I'd have to accept the Default layout and then remap my desired traits and save as a custom config with some name.
I found it most time consuming in the Stable / Public release oddly and not to frequent in the 3xperimental branch of the game. A change ratio of 3/10 as opposed to 10/10.
It did become one of the things that with time and effort and repetitiveness: I became faster. Confident to navigate the mini app and tested even more tweaks.
I have had to deal with this game resetting my controller config and making my layout [Incompatible config] with every major update.
Getting real tired of having to remap my layout again, and again, and again, and again.
I eventually developed a solution for it and dealing with the excess layouts that are created.
It's a bit involved but it gets rid of the extra layouts and you're able to set up your controller config the way you want it ... again.
https://steamcommunity.com/app/275850/discussions/0/3811782223873687465/#c3801650943419041739
I've collected a few for you and re-posted the comments. The links should take you to the actual thread for additional comments.
I think the recent update added support for 8 mouse buttons so I am just guessing it may have added some conflict to controller input. But usually after any update that adds any new functionality to controls, it can help to attempt to clear out every old or in use controller setups and then build fresh customisations, after downloading the developer Official Setup (which hopefully is current and should be updated).
I recently had your same issue and solved it by clearing things out and rebuilding my customisations on the official setup. No changes to my old set up configuration but things work now as expected. I saved the setup as a personal save and also a local save and as a community save to 'download' to another steam account on the same PC, which was not registering the personal save. The community save took a while to filter through to the server but after downloading, the other account controller also worked again as expected, without the tedium of rebuilding exactly the same customisation again.
I don't use cloud saving (or try not to) to avoid setups being saved or not cleared that may be overriding new saves. Anyway making new setups, when switched to Steam Big Picture Mode should help. It is a more reliable or robust method. Once everything is working as expected and the new configuration setup is loaded correctly starting Steam and the game, then leaving Big Picture Mode should be okay if that's preferred. One useful thing about playing the game with Big Picture mode in use, is that the controller can also be used as an input for text, when entering new discovery names, similar to entering text as with a console with controller.
Lastly, in the Big picture mode controller configuration menu, there are tabs at the top to switch between, personal, local and community saves and so on. Also it can be easy to miss the other button at the bottom of the menus. This when toggled will display 'other' setups not initially listed. Another guess but there may also be a slight delay before saved community setups populate and become visible in the lists.
On the old steam UI, there was a warning I remember that wanted the setups to be played for a short time before they were permitted to be uploaded to the Steam server. That may still be relevant but there seems to be no written info about that now. Also it is not clear which set up is currently in use. Although there is a blue vertical line next to the setup I think is in use but it is a big buggy and not always present when needed! It can help to switch to the new official setup first, then after a steam restart, more reliably be able to delete any old setups not in use that you own. To do that select the old unwanted setups from the list, using the D-Pad and follow the help buttons on screen info.