I read that the reason the model was pulled from the ready room set was so it could be used as a reference for Jein's team to construct the Stargazer filming model. In one scene, Levar Burton does say "Constitution" class, so they were planning on using the movie model, but couldn't get it or something, so they decided to build the model based on the kitbash, and then dub over that line with "Constellation".
Yeah, what I think happened was this (and someone more in the know can correct me if I'm wrong): They did indeed pull the model so that Jein could use it as a reference. However, during filming of the episode it was determined that Jein wouldn't have the filming model done in time for the post-production VFX, so they filmed the ep with the intention that the Stargazer would be a reuse of the TMP Enterprise (the TMP desktop model, Geordi saying "Constitution class," etc.). But Jein did have his model ready by post, so they went back and dubbed over Geordi's line before the ep was broadcast, and in subsequent episodes the yellow desktop model was returned to the ready room.