Hello,
Substrate do not enable itself so not sure how that happened. You should then disable substrate for your project. If you have not resaved any material when Substrate was enabled, it should work the same way as before. Otherwise, substrate is a one way ticket, so if you did save some materials you will have to do some rewiring yourself.
Otherwise, fixes have gone in for Slate materials + Substrate in 5.5 so that error should go away.