Well, this could be tough----or it could be just a nasty timing thing to make you think the roof was the cause! Gremlins have ways to confuse us, so keep that in mind!
But tell us a bit more about the process for the roof overlay. Were new fasteners of some type driven into the Rv and where? Glued on? What are the odds of that process driving a fastener into wiring?
For starters, this is your 12VDc coach wiring drawings where the furnace, etc is shown and I do spot a "suspect" for checking but it does bring some questions:
https://www.winnebago.com/Files/File...ire_137067.pdf
You mention ceiling fan, is that the bath vent fan or something else as I see the bath vent fan connected. Are we speaking the same thing?
Sheet two has this info. There are three wires on the furnace shown at top left and it looks like wire "JB" is the battery, with "JM" being the ground going directly to the ground bus bar. Possible removing the Wire JM from the bus bar would clear the fuse blowing (short?) and tell you something?
Sheet 2 frame 2 (S2F2) shows these wires also go to the vent fan, so it may get into needing to disconnect these two items from the wiring to find if the short is in the wiring due to damage or if it just happened that one of those failed to give the new short you are seeing???
And the last snip does show these going to a breaker. The drawings are shown looking at the backside if I am correct, so does that fit what you are finding blown or tripped?