https://bugs.python.org/issue41545 is a duplicate of this.

In that report, there's an example of something that can go wrong with the save-a-boolean-per-context-manager approach even when threads are not used, but when concurrent generators are used, like

def gen():
    with gc_disabled():
        yield 1
        yield 2
        yield 3

a = gen()
b = gen()
next(a) # disable gc
next(b) 
list(a) # this re-enableds the gc
next(b) # gc is enabled but shouldn't be.

A counter for "number of times disabled" may be a better approach.