The builders are coming back tomorrow?
What does the builder say is causing the movement?
Obviously he thinks that changing the plywood is going to solve whatever the problem is,
but as you've seen already, there's a few other things to consider.
I think you should do a bit of detective work tomorrow, take some pics of the removed tiles and get a few on here.
Once the floor is removed, then describe the situation and assess best preperation methods on here, and with the info you've already got you can tell the builder to hang fire with the tiling untl its all prepped correctly..
Also, Usually you'd have to beg and argue for the builder to fix things - but by the sound of it he's happy to re-do it, maybe he know's something that we don't?