generally you send a watch to the service centre and get an estimate. if you dont want the work done or dont want to pay for it then they send it back. if you authorise the work they fix it, you pay and you get it back ..simple.
Chopard appear to have worked on your watch without your authority and ou should tell them that telling them that you want your watch back with its original parts refitted. obviously they cant do this as they've thrown them away so you should tell them that you want your watch back, end of story. if they've chosen to do work without your authority thats their loss. do it in a nice way and point out that you've owned the watch for a long time, had it serviced by them every 2 years and should be considered valued customer so parhaps a bit of good will on their part would be appreciated.
its a lot easier to say it than do it, but you can always send a solicitors letter as a last resort.
the issue of water ingress is a different matter. if its still under repair warranty you should be fine, but if not you really havent got a leg to stand on IMO.
hope this helps
Graham