In the interest of being humane, you might hold off on any major prunes until after the young are out of the nests, which is just kind of good business anyway as that is about the same time that bird nesting is happening.
It’s been a while since I’ve been involved in forestry work and while I personally don’t have a vendetta against the little guys, many people do. I have to admit that they have been problematic to the forestry/conservation work I’ve done in the past, as they do like to girdle tree tops and strip the bark off the leaders. Generally speaking, when I was doing that kind of work, we generally continued with indifference to their presence, particularly if it involved an urgent safety prune or safety removal where a particular tree presented a clear hazard. Usually we didn’t see many external nests though, mostly we found them in cavities in cotton wood or willow trees.
What is the issue you are dealing with that might require an actual SOP for fox squirrels? Would it be possible to keep a nuisance wildlife expert on hand to utilize some techniques to encourage the squirrels to leave the nests before you prune? There is certainly no shortage of habitat for the little buggers.
City of Northglenn