Some questions and then easier things to check first:
?1. Were the batteries at 12.6V immediately prior to cranking & fail to start?
?2. Selector was in "both" position when cranking?
?3. After removing batteries, you placed them on charge - one recharges, & other did not - have I got this right?
?4. Fuel valve was open, and decompression lever closed when cranking failed to start?
you would not be the first
INITIAL QUICK TESTS:
With battery switch off (batteries installed, but positive cable not connected), place ammeter between Battery positive (+ red meter lead) and Positive (Red) Battery Cable. Read no current - OK. Read any current, look to your starter wiring (short to ground).
Turn Battery Selector Switch to "Both", ensuring all DC Panel Breakers are Off, or Fuses removed.
Read current as above. No current - OK. Any current - look to panel feeder.