It sounds like something shorted when you changed the batteries. One of the transistors or SCRs might be bad. Do you have a manual / schematic for the machine? If not, there is one available on IPDB;
http://mirror2.ipdb.org/files/871/Williams_1979_Flash_Manual.pdf
As phil-lee mentioned, post this issue in the Early Solid State forum and we'll meet you over there with some more suggestions:
https://pinside.com/pinball/forum/forum/tech-early-80s-solid-state