It seems that after I've crafted Samum, meditating no longer replenishes my potions and bombs. At first I thought that I'd run out of Alcohest, but I have 15 of that plus a whole collection of other alcohols.

Before this, I would get the notification that my stuff has been refilled when meditating for one hour, but now that no longer happens, regardless of how long I meditate. Since this has happened I've crafted Grapeshot and Thunderbolt, but that changed nothing.

I have no mods installed that change anything about alchemy, only friendly HUD. Is there anything I can do to fix this?

Have you tried verifying the game files ? Couple of other bugs can be fixed by using the 'Verify and repair' option in GOG Galaxy. It's worth a try.

That's a good idea, but it wasn't a HUD glitch, the 0/3 is accurate. However, it is actually the mod that prevents potion refill. It's not supposed to prevent it but that puts the bug with the mod and not the game. So, sorry to bother you!

It's no bother. The important thing is you now know what's causing it.