These are another strange bugs (the strange ones are the best :D )
In the general settings of a desktop/folder, in the item actions, set ‘launch shortcut [select shortcut]’ in swipe, tap, whatever.
1)In a specific item set in that action another different shortcut. It is still not marked as custom, so if you change the general, it is also changed.
2) if you set a different action, and then you uncheck the ‘custom’ checkbox to reset it, it ask about which shortcut you want to launch, instead of remember the general you set before.
It seem that the launcher just remember that it launch a shortcut, but not which one (I’m talking about custom/non-custom, of course the launcher know which shortcut execute)
Am I right? Could it be possible, in some way, to check if they launch the same shortcut when deciding if they are the same or not? 
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D5 Creation
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I took me some time to understand the problem, but now I think I have got it, thanks 😉
Indeed, the custom “detection” is done on the action type only, and does not look at the action data (in that case: action type is launch shortcut, action data is: what to launch).
I think it can be fixed !
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