This problem happens when using your mod. I posted on the forums.
I was forced to un-install Whistle Stop Factories, even though I really like the mod,
But its seriously causing havoc on my Crafting Page.
.
https://forums.factorio.com/viewtopic.php?f=5&t=67082&p=409261#p409261

I'm really sorry the bug caused you that much frustration. This was reported by someone else a few days ago. I share your frustration as I spent about 3 hours trying to troubleshoot. This bug has been difficult and inconsistent to replicate.

This has to do with the hacky way in which I hide my alternative recipes. Originally, I had no way of hiding my recipes and everyone using my mod saw duplicated crafting categories (as that was better than seeing double within each crafting category), but then someone suggested I could disable all my recipes UNLESS you had a whistle stop GUI open, so that is how I'm currently doing it, but it is a bit hacky, and may be why its a bit buggy too.

An alternative solution for you is to open/close a whistle stop GUI. This will reset all the recipes to hidden. This worked for the other person who reported the bug. Unfortunately this isn't an ideal solution, and I'd still like to get this fixed.

In the meantime I've bumped a request I've had to the developers to add a flag to recipes to simply hide them from the main crafting window, which would mean I wouldn't have to solve this with my hacky way. I also came up with another idea for troubleshooting this issue, so will take another look at it and see if I can't figure it out.

Thank you <3
I like the mod a lot., And it gives me huge incentives to use trains for these factories & refineries.
but in the meantime, I will wait until you release a new update before I use it again :D
Again, thank you for responding and understanding my situation. :D

And as far as the ideas as the solutions, I was thinking the same thing.....LOL
I guess someone beat me to it....LOL anyways, I will have my eye out on updates of your mod. :D
Thanks for being awesome. :D

I finally figured it out and apparently when I went to go report it, it has already been fixed. From the 0.17.9 changelog:

Fixed that mod settings could get scrambled/reset when adding removing or changing mods.

That was the issue. The recipe-hiding was getting turned off when adding/removing/changing mods. Thanks again for your report!

Thanks :D