No. Of course. They were simply bypassed using two large paper caps which match the specs. I guess this was/is common practice. I imagine I'll just replace them the way they are, and probably bypass the third can as well when I recap.
As for the caps not in the schematic I had decided already to go with what is in the chassis vs the schematic. All of the original caps in there have Philco part numbers on them so for the ones that don't have specs printed on them I should be able to pull the specs off of the schematics from other Philcos from around the same year.
The only other quick question I had was about the way the RCA input is wired. It has two wires coming out of the back of the input jack and both wires are sliced together like a 'Y' before leading. It works, but the wiring just seems strange to me.
Toxcrusadr - I don't know if you are thinking of restoring yours or not, but in case you wanted new buttons this guy seems to have the best price I've seen around.
http://www.antiqueradioknobs.com/partlistings.html
The 1941 Philco Pushbuttons will fit the 39-25.