Towards the end of the Dominion War, the founders and the Great Link become
infected with a disease, that we later learn was planted by Section 31 through Odo, and infected to the rest via linking. Odo linked with the Female Changeling at the beginning of Season 6,
and from that point the wormhole was impassable to the Dominion (due to the mines and then the wormhole prophets), so how did
he or she pass the disease to the Great Link
?
The disease is transmitted to the Great Link when Odo visits it in the Season 4 finale "Broken Link". From the Trivia section:
Presumably, Section 31's plan to have Odo infect the Great Link with the morphogenic virus he was infected with during "Homefront" comes to fruition in this episode, although it would not be until the seventh season episode "Treachery, Faith and the Great River" when symptoms of the infection would begin to show themselves. Dialogue in this episode implies that it was the Great Link that caused Odo's ailment, not Section 31; the script for "To the Death" reveals that Weyoun infected Odo with the virus that afflicted him here when he slapped Odo on the shoulder during a conversation, making his illness here different from the virus created by Section 31.
I suspect you may have a slight misconception about the course of events.
Odo was infected (as a carrier of the morphogenetic virus) by Section 31, presumably during his trip to Starfleet Academy during the episode DS9: Homefront (Season 4, Episode 11). Note that he submitted to extensive medical testing and a full scan of his morphogenetic matrix.
Odo became part of the Great Link in DS9: Broken Link (Season 4, Episode 26). This is when the Founders were infected. Odo remains unaffected because he's only a carrier of the disease.
The Female Founder was regularly traveling between the Alpha Quadrant and the Gamma Quadrant in the early part of Season 5. This presumably is when she became infected, even if she wasn't before.
The Wormhole was disconnected in DS9: Sacrifice of Angels (Season 5, Episode 5).
After Odo regained his shape-shifting powers in DS9 : The Begotten (Season 5, Episode 12) at which point his disease switches from merely being carried to being fully active.
The only problem with that was during the the occupation of Bajor (First Part of Season 5), the Female Founder could not get back to the Alpha Quadrant thanks to Rom's self-replicating mines.
I'd guess that it was all during Homefront. Odo was infected by Section 31 and Odo momentarily fused with the Admiral/SeaGull/Founder to expose that specific Founder. If Odo is Patient Zero, than the Admiral/SeaGull/Founder would be Patient One, not the Female Founder.
