In the case where the files were deleted, I'm fairly sure I didn't touch Mercurial in between. I'll particular remember to pay attention to this from now on.
MercurialEclipse works by calling command line Hg. I'm not 100% sure how this command does what it does internally. I'll try to check if I can monitor the filesystem somehow.
About checking the timestamp, do you mean here to check the stamps of files that are still there in the deployment after a delete?