In the case of Stargate,
the cartoon spinoff got erased from continuity, so that could partially qualify.
The animated spinoff SGI is not a part of SG canon, but it aired between SG-1 and SGA. One could argue that had SGI been more successful, it would not have been disowned like that, and possibly SGA and SGU never would have come to pass (instead we might have had something else). Of course, SGI is a cartoon, and doesn't have essential characteristics of a reboot. However, to everything that aired after SGI, SGI never happened.
IIRC, SGI was made by different people to the live-action series'.
Although he's now talking about a fresh reboot (owing to the age of Kurt Russel and James Spader), Roland Emmerich talked a bit a few years ago about making 2 sequels to the original Stargate movie, which would have ignored all the TV spin-off series. Although not a true reboot, Stargate SG-1 did make several big changes to the original movie's backstory and going back to the original premise would qualify, I think.