I am fairly certain that Green could win any court case that challenged that he still owns the copyright. The initial Bored Ape Yacht Club contract would actually need to include explicit provisions for what happen if the token is stolen. Otherwise a US court would invalidate the illicit transfer of rights based on standard contract law.
Possibly? Copyright law intersects with my work in weird ways and at this stage I truly believe "copyright" means whatever the highest priced lawyer says it does. I want to claim that BoredApe giving Seth Green the copyright as a package with the sale of the NFT is something that would not extend to the next owner unless explicitly agreed upon, but I've been very wrong before.
At any rate, getting the actual string of code back would require finding the thief and then getting the location out of them which is pretty unlikely. Even if Seths lawyer says he retains the copyright, if that is in dispute in any way it could torpedo any potential contract that requires that copyright since a challenge at a later date means months to years of litigation. Challenges to copyright typically happen after the work has been successfully used, and the number and strength of lawsuits increases proportionally with the level of success.
Or, Seth saw the way the wind is blowing for crypto in general and is using this as an easy way to no-fault break his contracts.