Thank you for the information Erika and for the testing.
The reason why I had asked was because prior to 10.6 there was an issue with services that had longer names that caused a create replica failure during a download. This wasn't a Collector issue specifically, rather a Portal/ArcGIS Server issue. However because you're running a newer version, that wouldn't be the issue. Besides all your service names are fairly short.
Please let me know if you run into this error again. If so, and if its using the map you shared with me already, please share any repro steps if necessary.
If you cannot reproduce the issue in this map, perhaps create another test map that includes only those 'removed' layers and see if you can reproduce the issue in that map. Perhaps the issue can be narrowed down to specific services.
Thank you
-Kevin