Hi Arie,
Theoretically, existing connections shouldn't be affected by a change to the iRule--they should continue to use the old version of the iRule. Spark commented on this in a post here:
iRule not applied immediately
http://devcentral.f5.com/Forums/tabid/1082223/asg/50/showtab/groupforums/aff/5/aft/1168308/afv/topic/Default.aspx
But I and others have seen some odd behavior when updating iRules on actively used virtual servers as described in the post. If you're able to reproduce the issue, you could open a case with F5 Support and ask them to help you investigate the issue.
Aaron