I can comfim that the weapons dont get deleted
nore do the weapon mods on weapons.

for example
i set my main recon soldier to train as a leader and give her the "come get some skill"

>>> this in turn <<<
DOES un-equip the former weapon she had
(mine at the time was a tier 2 autoloader on my shotgun)

while the main recon soldier was training,
i planed on passing the formerly equiped shotgun to the 2nd recon soldier i had.
(normally goes in order from top soldier to bottom)

when i bought up my 2nd recon soldier
i noticed that she had the 1st soldiers shotgun equiped

--- hope this helps you'll with this issue ---
@Long War Studios or a moderator
not sure if this would help, but maybe one of you could consider placing this as a stickied thread so anyone whos having the issues with "deleted mods" would hopefully see and read this

:)