I think the agent was trying to pull a fast one. Or he is a moron, or both.
Either side could have achieved these results if that is what they wanted. Broncos could have just cut Doom without offering pay cut. Same result. Agent could have refused pay cut, forcing release. Same result.
But with the agree, then delay, then send a couple minutes past deadline, the agent could have tried to get Broncos to miss both the contract deadline and the release deadline which would have resulted in original deal staying in force, and Doom getting $12M salary for 2013.
As for what they can do to rectify this if both sides want to, Doom could sign a free agent deal with Denver that approximates (closely) the fubared deal that missed the filing deadline. Would have to be something like $3M base (2013), $5M signing bonus, 3 year deal. Cap hit for Broncos for 2013 would be the $4.8M accelerated from release plus $3M base plus $1.7M in prorated signing = ~ $9.5M....Doom still gets $3M base plus the $5M bonus (= $8M salary they had agreed to). Not perfect but close. But the issue is whether Doom and agent would do that before checking the market.