If you have a traditional project and you remove a project member
there observations will also be removed from the project. The only way
to have a member leave a traditional project but keep there
observations around is to have them leave the project and check either
of the options other than "Remove all your observations from this
project" when they do so.
Have you considered instead using the new 'collection style projects'?
They allow you to select the users's who's observations you want to tally, e.g.:
https://www.inaturalist.org/projects/southwest-texas-inat-a-thon
tallies observations made by tiwane sambiology alisonnorthup
nanofishology etc. made between April 4 and April 8 2018
You could make a project where you add/remove users based on whether
they're currently enrolled to tally the current class, and another
project where you only add users to tally everyone who's been
involved.
Or you could even make a separate project for each class and put them
all under a single umbrella to compare across classes e.g.
https://www.inaturalist.org/projects/city-nature-challenge-2018
you can read more about collection and umbrella projects here
https://www.inaturalist.org/blog/15450-announcing-changes-to-projects-on-inaturalist
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