I don't know how often this happens in other multi-show franchises, because I don't watch any of those, but it really gets on my nerves when actors who have had extended runs as a character in the JAG/NCIS universe return to the franchise years later as a character that has nothing to do with the character they originally played. First, they had Zoe McLellan, who played Jennifer Coates on JAG, returns to the universe in NCIS: New Orleans as agent Marilyn Brody. Then, Karri Turner, who played Harriet Sims on JAG, makes a return as a guest star on NCIS as another recurring character's aunt. And, most recently, Scottie Thompson, who had an extended run as Jeanne Benoit on NCIS, returns as a guest star on NCIS: Los Angeles, but as a government contractor.
The most egregious of those to me is Karri Turner, because technically she was actually on NCIS as Harriet Sims (she appeared in the show's backdoor pilot). The actor who played her husband on JAG has made multiple subsequent guest appearences on NCIS, reprising his character... so why not Karri?