Thanks for the reply, Starrodkirby86.
I did some googling about this problem and it looks to be very common. Unfortunately I didn't find anything particularly useful online in regards to a solution but I did a bit of fishing around myself and figured out something that might be of use to others. This might be able to help anyone in future that has the same problem... but I'll say now that it still involves some work (a lot of work if your game is significantly developed).
What's happened is that for some reason, when the program glitches like that it wipes the file RPG_RT.lmt (or it might have been the RPG_RT.ldb one). You can look at the file properties in windows after you get the error and see that it has a filesize of 0 bytes, just to make sure which one. The file in question seems to be where the stuff in your database is stored. While there is no way to retrieve the lost information, you can do what I did and get most of your game back.
You need to copy the corresponding file from the sample game that comes packaged with RM2K (or alternatively, if you have deleted the sample game, create a new, blank project and save it so you can use that instead) and place it in your game's directory.
Here's the heartbreaker: Your database is returned to default. That means all your items, attacks, battle animations, monsters, party information, names of switches, etc. are set to those of the sample game. This causes some association problems that unfortunately you'll have to use your memory and a lot of research to resolve. For example, let's say you had item number 1 set up as a sword. In your game any event that gives you the sword will instead give you the default item it's been returned to. You need to go through all your events, shops, etc. and write a list of what has been changed to what, and manually create them all again in the exact same spot. Same goes for monsters and monster parties, so you'll need to check all your areas again and work out which enemies you had in what slots. Make sure you use a fine tooth comb and go through every single thing, or you're gonna have some strange stuff happen in the future.
The GOOD side of this solution is (apart from actually being able to open your game) that your events still all work correctly, even those that use switches. All that's changed where switches are concerned are their labels, which unfortunately will be a little confusing if you use some of them commonly and need to select it for new events. Once again, you need to look back through all the significant events again if you want to determine which switch was which (we're both poets), and rename them to something you'll remember. The best thing though is even if you don't do this, you can play your game and you'll notice that all the switches work correctly. The functions of your switches are stored with the events they are used in, seperately from their labels, so luckily you don't have sample game events happening randomly. What you do need to do, however, is remove the sample game common events and put your own back in there (if any).
It's sad to lose so much but this way, at least you don't have to start from scratch. You still have your maps, and you still have your events (except for your commons)... and if you're like me, you use a lot of events. Losing my events would have basically meant I'd be better off making a new game anyway. This way I didn't have to!
Wish I could have came up with a cleaner solution but for now this is all I can find. I'm trying to work out what causes it... but you are correct that it is not the apostrophe. In fact the sample game has an enemy called Will'o'wisp already. For now, just make sure every time you finish something significant that you copy your game's directory and paste it into another folder somewhere as backup. Hope this helps anyone else with this problem!