Further to my earlier email, I suspect that the slowness is due to gradually accumulating cruft in internal data structures. Maybe not a memory leak but conceptually similar, possibly fragmentation or lists that accumulate stale junk.
I had my thesis open, and editing was sooooo sloooow. I created a new document, and typing in this one I found out that editing was also just as slow. Hmmm, I thought, and closed my thesis. Again, editing the new document was painfully slow! I restarted LyX and created a new document - problem is gone. Even after opening my thesis, problem isn't apparent. It looks like you may have to do actual editing of an actual thesis to reproduce this! (Hence I'm sure some of the developers are wondering what I'm on about.) Have fun, Darren