Did you fiddle with altitude correction at some point? If so, this might explain:
If not, then I’m stumped because AFAIK, if the Altitude gain field in the FIT is populated by your device and altitude correction is disabled, Intervals will initially simply use that and not calculate anything. Once that field get’s overwritten by altitude correction for example, a revert will have Intervals calculate it from the available elevation stream with it’s own algorithm and small differences can show.