It has not occurred to me to look at it this way, but just like Shirley Partridge's youngest son "changed" from a brunette to a blond in one season, her father changed from a hip older man with gray hair on the first episode that Shirley's father appeared, to a short chubby mustached man with a balding head and strong burly arms on a later episode in which he appeared. Shirley's mother remained the same.
I don't think that it was mentioned that Shirley's mother remarried.

You know what is ironic?

Ray Bolger played Shirley's father minus the final year. He of course is best remembered from the Wizard of Oz.

In the final year, Reuben's mother was shown. When I did some research on who the actress was, I learned that she played the Wicked Witch from the Wizard of Oz. She appeared just a few episodes before the Shirley's parent's were shown the final time. Jackie Coogan played the 2nd father.

Shirley's parent's had more stories than Chris & Tracy combined.

Of course there should have been another set of grandparents. But since I have never heard the Partridge's father mentioned, no surprise no other grandparents were mentioned.

So Margaret Hamilton( The witch in the Wizard of Oz) played Ruben's mother.