Well that would be a major issue in any title which should be immediately addressed no?
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It might be an idea to slowly build a fresh profile from the ground up. Checking along the way that there are no functions duplicated to other peripherals etc.
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Peripheral disconnect resulting in CTD was actually fixed in SU5 however there seem to be reports that the bug may have been reintroduced in SU7
Therefore if your joystick is disconnecting during gameplay this might cause FS2020 to CTD.