Merritt confirmed today on Twitter that no retention funds were used in the recently announced extensions:
Bob Kellett @bobkellett
@MerrittPaulson Curious if any retention funds were used in the recent contract extensions.
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Without really knowing how the Retention Funds work (or knowing the specifics of how exactly GA contracts remain off-cap over time, in the case of Nagbe's extension), we can't really speculate about why that was the case. But it's contrary to the speculation of many Timbers fans when the extensions were announced about the time we learned that Retention Funds exist.