Save your etkey and etconfig before trying anything else. You can find these from C:\Users\xxx (your username)\Documents\ETLegacy. Etkey is under etmain, etconfig is under legacy. You'll need these later.
Now, if you are using a Legacy client:
-> Navigate to C:/Program files (x86)/ETLegacy
-> Open "uninstall.exe" and uninstall the whole game. It will ask whether all user files should be removed -> remove all.
-> Download the latest release from https://www.etlegacy.com/
-> Install the game and launch it.
-> Move the saved etkey and etconfig to the previous locations. Replace the ones already there.
Try the game now. It will have to download every .pk3 again but this time there should not be any issues. If there are, let us know.