The config file seems to be resetting whenever I open Minecraft, making it impossible to modify the potion recipes. It's resetting even if there's no changes.

Looks like I made a bad choice of type to use to store potion map settings. It basically didn't allow any changes to the list of potion ingredient items, only to the effects.
I have changed that now and will be releasing a build in the next days. However if you want to test this out you can also use a dev build from https://bintray.com/p3pp3rf1y/maven/download_file?file_path=Reliquary-1.12.2-1.3.4.725unstable.jar

The config is still resetting after reloading

It looks like the configs didn't reset but Notepad++ is saying it did

It seems to work now but I'll do some more testing with custom potion effects

I've been getting crashes with Extra Alchemy potions

Any crash logs you could share?

The crashes were caused by incorrect potion names. Everything works now but I can't see any potion essences when I search for them in JEI. I have it so that it displays all combinations when looking at ingredient uses.

Could you link your config so that I can take a look/test with it?

https://github.com/belathus/Wanderlust-Renewed/blob/master/config/xreliquary.cfg

so the ingredients load properly, but what you're hitting here is a setting in JEI that will stop displaying all subtypes of an item if the count of those is greater than a value, by default 500;
Search for I:maxSubtypes in jei config and set that to (much) higher value to see these.

btw, I have released the version with corrected loading of potion map from config and have tested your config with that version and could see the potions there