Hello Adam T,
It’s one of these features that are required by some users, and cause significant problems for other users. It’s on our to-do list, you can follow it here: https://bitbucket.org/axantum/axcrypt-net/issues/191/add-option-for-recursive-operation .
I can’t promise any delivery date for this, but it should not be too far off. It’s much requested and it’s not really that technically difficult – although there’s more to it than it may seem…