Big-hitting Lynn was named on Monday night as one of several high-profile overseas stars to feature in the UAE tournament, which will directly clash with the Big Bash.
A number of BBL draft nominees were also named, meaning they will only play in the first half of the Australian competition before flying out in early January for the UAE, where the teams are now owned by cashed-up Indian Premier League franchises.
Australian officials have long expected that would be the case with draft players and planned around it, with the exodus likely to come at the same time Test stars return to the BBL.
But it is the inclusion of Lynn in the UAE's list that does not sit comfortably with CA.
Under ICC rules, every player competing in an overseas T20 franchise league requires a No Objection Certificate (NOC) from their home board in order to feature.
While Lynn no longer holds a national or state contract, Australia would still be considered his home base by the ICC.
CA officials had yet to receive a request for such a certificate for Lynn and made clear there is no guarantee it would be granted.
"Cricket Australia has not received any applications for NOCs pertaining to a player's participation in any overseas competitions for the upcoming season," a CA spokesperson said.
"Our guiding principle remains the prioritisation and protection of Australia's domestic summer of cricket and the interests of the game overall."
The current players' deal also outlines that NOCs are usually only granted outside the Australian summer, be it at the conclusion of state cricket for the IPL and grade cricket for all other leagues.
Lynn's management, the players' union and UAE league officials are aware of CA's position.
Let go by Brisbane at the end of last summer, Lynn would still be a crowd-puller and magnet for TV audiences at any of the eight Big Bash franchises.
There has been interest shown and even talks with Adelaide, however the reality is no club could match the maximum salary of $650,000 on offer in the UAE.
CA also have some question marks over the validity of the ratification of the UAE league, given a whopping 72 overseas players will be welcomed with 12 in each squad.
The issue was raised at a meeting last month of national association bosses, who believe the ICC charter dictates an allowance of only nine overseas players per league.
BBL draft nominees on the UAE list of incoming players included Alex Hales, Sandeep Lamichhane, Mujeeb Ul Rahman, Evin Lewis, Colin Munro, James Vince and Dan Lawrence.
In better news for the BBL, positive talks remain ongoing about David Warner's return to the BBL, after having last played in the Australian league in 2013.
9°C