At the moment a re-index is triggered the indexes are removed, so the repository can start to be indexed again. That being said, you wouldn't be able to stop it and go back to the state it was before.
I'm thinking however in a way to try to reduce the time it will take to be fully indexed by restoring a backup of the indexed of this repository. Would you have a backup by any chance? The indexed are stored at
$FISHEYE_INST/var/cache/<repository_name> so I think a recent backup would help to have most of the repository already indexed, so FishEye could start from this.