Regenerating snapshot and reinitialise subscriptions wipes out permissions?

Hi

I have just regenerated a snapshot on my source server and reinitialised the subscription on the destination.  Before this, I had permissions set up on a couple of SPs on the destination server.  It turns out that after reinitialisation, the permissions have been wiped out.

Is there any way I can avoid permissions being affected in the future?

Thanks in advance.