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When a modifier was animated by a NLA strip, this animation was not working when using the old depsgraph. This was because the code which checks if a NLA strip affects any modifiers was missing - specifically, it was originally left out as it was thought that it was unlikely that many users would need this, but adding in those checks would have a (slight) negative effect files where there are heaps of NLA strips but modifiers animated this way were absent. The new depsgraph however doesn't suffer from this problem, as these sorts of checks need ot be built into the graph-building stage for everything to work, so these links had already been added.