I was finally starting to make some progress in MM1, but now something weird is going with my Cleric - they currently have 21 HP, but their total HP has dropped to 5. So basically, if their health drops below five, there no way to get those lost points back again. I've been unable to find an in-game explanation for this(it doesn't seem to be a curable condition), so I'm guessing it's a bug. Is there an easy fix for this, or am I going to have to resort to hex editing to sort it out?

Have you visited a temple? It might be illness or poison, which can be cured at a temple. Another thing to check is your cleric's age. Your cleric may have been aged by some magical creatures, causing stats to drop dangerously low. If so, the best way to reverse aging is the rejuvenation spell, which is a high-level cleric spell. If you don't have that spell yet, there are certain places in the world that will temporarily grant you all spells and then you can cast it. There's also another way to reverse aging but it's much harder.

Healing at the Temple won't fix the problem. It refills the affected character's HP but the max HP is still as low as it was before.

It seems like whenever I rest after a character has been afflicted with Poison status, their max HP becomes equal to the amount of HP they currently have. E.g. - my fighter had 42 HP before becoming poisoned, but only 22 at the time of resting - 22 / 42. After resting both HP levels were now the same - 22 / 22.

It's incredibly frustrating. I can't see a way around this other than starting over again, or just going in with a character editor and putting the stats back to what they were before.

It's definitely not premature ageing, none of my characters are older than 21.

I'm not certain, but there might be a difference between healing (i.e., refilling hit points) and actually curing the poison at the temple. Try messing around in the menus at the temple a bit. Make sure you are actually removing the poison status effect. If that doesn't work, you can try the spell to remove poison. If you don't have that spell yet, then I can guide you somewhere that will grant you all the spells temporarily.

I do remember that max HP thing... resting while poisoned lowers max HP. But after I had it cured at a temple, and then rested one more time after curing it, my max HP returned to normal. Are you absolutely certain this doesn't happen for you? Make sure you rest after getting cured at the temple, and make sure the temple is actually curing your poison and not just healing your lost HP.