Doubt the battery but anything is possible.
Id be leaning more towards losing the 5V standby and/or a short. For it to be working fine then not working after "tidying up" screams loose connection or short.
First thing I would do is pull it all out and put the board on a box and add components one at a time.
CMOS battery shouldn't come into play unless all power is removed.
“Two things are infinite: the universe and human stupidity, I'm not sure about the former” ~ Albert Einstein