I found this thread after having a similar experience with two different n900s. The recommended fixes work well, but unfortunately they don't do anything to prevent the problem.

From my observations, there seems to be a definite correlation between receiving multi-part SMS and corrupting the conversations database. (By multi-part I mean a text message so long that it has to be broken into two separate text messages.)

I have tested this on two n900s (both on T-Mobile USA), and the correlation is practically 100%.

Sometimes the problem doesn't appear on multi-part text messages sent between two phones on the same network. However, EVERY time my n900 receives a multi-part SMS from a phone on another network (Verizon, AT&T) the associated conversation thread disappears. At that point, the only solution is to erase the thread, or repair it as described earlier.

For me, a workable solution has been to immediately erase any SMS conversation thread that receives a multi-part text message. It's annoying, but it works.

Hope this helps.

(Also: thank you to everyone who posted other fixes.)