I usually don't bother trying to reload transports.  I usually put them on a planet when they get depleted and decommission them.

Any legions left, re-enter the pool and I build new, usually better transports.

Note:  Its usually faster to move legions by decommissioning transports from old wars on the other side of the galaxy from the current war, then to move them across your space.  I build new transports on the current front line with the re-pooled legions.

Hmm, I thought that if you docked at a starport, then when you ejected the transport you'd get a chance to reload legions.  I'm nowhere near being able to try that out on the 2.6 opt-in, though, so I can't verify whether it's working or not.

"I thought that if you docked at a starport, then when you ejected the transport you'd get a chance to reload legions."

I've tried this and it doesn't work.  

"Crusade 2.5, 2.6, or what?  It might have gotten broken in 2.5."

I've never gotten it to work for shipyards.  <shrugs>

Understood, that's why I thanked you for your reply. Wasn't sure if the mechanic had been changed and someone knows the new way, or if it had been disabled and thus, as you say, only Stardock knows the answer.

the only times i have been able to adjust transport legions after initial launch seemed to be when i had only 1 legion left on the transport (same amount it would have normally open creation from a shipyard). i can't honestly recall if it worked with multiple modules or not (those launch at 1 legion per module). unfortunately landing on those exact numbers can be difficult. more often i would just attack with the partial transports first next planet.