I'm glad you figured out a hacky solution to your issue. I assume newly unlocked recipes still work?
When WSF upgraded from 0.1.16 to 0.2.0, the logic for how recipes got unlock changed significantly. Before, in order to "hide" the recipes from the player crafting menu, I had to disable the recipes and then enable them whenever you opened a big factory recipe GUI. Because I just choose to enable anything that had a normal recipe currently available, I didn't need any special logic when new techs were unlocked.
But now they just added a new flag that allows me to just declare all big recipes hidden from the player crafting menu. So I could get rid of my hacky way to do it, but had to go back and add in a real unlock method. I'm currently using an on_tech_research event and scan the tech for recipes and unlock the big versions.
I'm not exactly sure how this all got messed up for you, but I'm guess my unlock switching method had to do with it. I should have migration code that enables all the big recipes that you currently should have unlocked when you first upgrade to WSF 0.2.X.
Anyway, in the future, another potential fix if recipes get messed up for you is to run:
/c game.player.force.reset_technology_effects()
(which, being a command, will disable achievements).
Outside of that I'm not really sure how my migration should've or could've been better handled to prevent this as I'm not really sure what exactly happened. When I get some time I might do some test upgrades from 0.1.16 to 0.2.0 to see if I might be able to replicate your issue, but other than that, I'm not sure how to help. I do appreciate the report though.
I might also see if I can replicate the conflict to see if that is something I'm partially responsible for.