I tried to make a glowstone block charge up the alkahestry tome by 9 units instead of 4. I did so by adding a datapack (using Openloader) that overrides the default charging recipes. That worked, but now I am seeing every charging recipe two times (with the glowstone block charging 9 units both times).

Also, I decided to make red sand dupeable using the alkahestry tome. I did it the same way as above, as I removed two other duplicating recipes and replaced the corresponding file contents with red sand/red sandstone duplicating recipes. Again, I am seeing every recipe two times (including red sand and red sandstone). The only ones I didn't see were the two I replaced.

On top of that, every time I do /reload, the recipes just add themselves, instead of replacing the already registered recipes. So I suppose that the issue might be in your recipe registry.

Forge 1.15.2-31.2.45
Reliquary 1.3.4.995

Probably a little late for you but I have this fixed in 1.16.5 dev version now - there was a problem with registry of alkahestry recipes that I keep on a side for performance reasons that it wasn't ready for reloads and data pack overrides of recipes. this is now fixed there.

this is now fixed in the latest release on curseforge