If I understood well, only transactions that are made while hard fork (around 12h pm gmt on August 1st) could never be confirmed. Once forks are separated, everything should be fine again in each fork.
If there is an hardfork, transactions could be nicely separated which makes it clear without messed it up.
If I'm right, only when there is a chain split (which is not hard fork), things could be tricky because at some point one of two branch will just be wipe out by the other which has achieve more computing power/ has the greatest difficulty of POW