Now I'm confused...
Rootsweb needs a GEDCOM uploaded to refresh anything on the WorldConnect Trees, so how did you refresh your Rootsweb online tree using FTM 2009.
FM 2009 can upload a new tree to Ancestry's online Member Trees but can't "refresh" anything as each upload starts a new tree.
Looks like you have two choices.
1) Export a GEDCOM from FZTM 2009 and use that to refresh your Rootsworld Connect tree and then delete the Ancestry online Member Tree.
2) Use FTM 2009 to upload a new online member tree and then delete the old online member tree.