Yes, two separate commands.

the press enter: this command calls the Conversations process in general. You actually DON'T have to do this step, but it reduces the likelyhood of some very unpredictable bugs that may or may not occur if you get a new message while the next command is in progress. I never bothered with it when I had this problem, but I suppose it is slightly safer.

Anyway, then:
This will take the database that stores all your message histories (the el-v1.db file), and will rename it to el-v1.db.bak. This way, you can later use some other database reading programs to dig up your messages from within the now-renamed file. Meanwhile, because it's renamed, the Conversations app doesn't know it's there any more, so effectively, all your messages are deleted. Next time you get a message, the program should be able to recreate a new el-v1.db file, and everything should work normally from there.

What this problem is is when the database that contained the messages gets corrupted. MOST of the time, deleting it and letting it get remade fixes it. Sometimes, you have to go one step up, and delete the entire .rtcom-eventlogger directory - that was what I had to do - remaking the databases themselves didn't fix anything, but when I deleted the entire folder, it fixed itself.

*Shrug* Just a matter of luck which one is the problem, but usually, it's the database, so just go with the above commands first.