I did assign a soldier to the interceptor because I assumed the aircraft would need someone to fly it, maybe that's where I made the mistake.
Saying that, once I unassigned him, the weapons, ammo and armour etc all stayed in the interceptor and there's some really good stuff in there that I can't access now.
It wasn't anything to do with the "transfer" function because I only had one base at that time.
Next time I play, I'll try selling everthing and buying it all again and see if it goes into the dropship.
Thanks for answering.