It’s the one that is most mentioned but there’s a lot. Any IQ field data (think W’ AlphaHRV, RespRate…), Garmin Firstbeat metrics (Training Effect, Stamina, VO2…) that have made it to intervals thanks to custom fields… You loose all that if you simply use the Zwift file. I would always prefer to keep that data iso the ‘virtual’ indoor speed/distance data which is fake anyway. You are on the trainer and not going anywhere 
The most complete solution to merge the files is fitfilerepairtools but it has a significant license cost. Gotoes does a very decent job at a lower cost (donation).
Both require you to download the Garmin and Zwift files and do some manual interaction before reuploading.
I’m not aware of any automatic solution.
I don’t have Zwift, but I every now and then use Zoffline which sends the recorded file directly to Intervals. So I download both Garmin and Zoffline fit file from Intervals, run them through Gotoes, reupload the resulting file to Intervals and then delete the originals. Result is a full Garmin file with map, speed, distance and elevation from Zwift.