Hi David,
The use of the x-refs in animation projects on cinema 4d for some they seem to work OK but for many they cause all kinds of quirks, xrefs are a good solution for smaller files and when you will work together with other 3d artists, But when you used in large projects, especially when it comes to moving rigged characters there’s just a lot of little inconsistencies
that often crop up when you least want them to, and are rather unpredictable, I don’t have a specific solution to your problem, but I will give you some advice that may be a reason to overcome what happened to you:
– set the file path to absolute instead of the default relative, also you can tried putting the xref file directly into the folder where your scene file is, maybe that could work.
– when you used XRefs for character rigs and for chunks of set during development, don’t nest them, nor make huge XRefs and save Xref’d copy of the scene now and then as insurance.
Hope that helps