richj and Robski:
The reason that Dynon's current advice not to connect Pin 2 (Keep Alive) to is that a software update somewhere along the way to the current software versions unknowingly (and apparently, un-fixably) rendered the connection of the Keep Alive / Pin 2 problematic - bootups became LESS reliable if Keep Alive was connected. With the Keep Alive disconnected, bootups became normal again. When troubleshooting intermittent bootups on Dynon's older products, one of the first questions their Tech Support asks is whether Keep Alive / Pin 2 is connected on the unit? If yes, try disconnecting it and see if bootups become more reliable.
The primary reason Dynon included the Keep Alive was to keep the clock circuit alive so you didn't have to manually update the clock every time you fired up the aircraft. With the advent of GPS units being connected to Dynon Avionics units becoming almost standard... and automatically setting the clock FROM a connected GPS, the Keep Alive became less necessary.
Because the Dynon backup batteries are Lithium-Ion, it's a bad idea to "freelance" the charging of them from something other than the Dynon unit. It's too easy to charge it wrong and generally just a bad idea to charge Lithium-Ion batteries from something other than the intended charger.
If you want to follow Robski's advice to connect, or re-connect Keep Alive / Pin 2... suggest you do so through a toggle switch on the panel. That way you can conveniently disconnect Keep Alive if you do have bootup issues from having Keep Alive connected.
Sounds like you need to connect the keep-alive line (pin 2 on the 25 way d-sub) to the main aircraft battery, via a suitably small fuse.
I believe that should keep the internal battery charged.
I do know it's advised to NOT connect it in the manual, but that's only an advisory. I guess your circumstance is one of the reasons it is an advisory rather than a hard and fast rule!
Re-reading your last post, I would guess that making up a simple d-sub lead with pins 1,2 & 3 connected (with fuses on 1 and 2) and hooking this to a 12v battery at home might work.
It does seem an awful faff to remove the unit from the aircraft to take home to charge when connecting pin 2 to the aircraft battery would do the same job.