If you can avoid it, I would not modify/extend the AnnotationManager, in this case. Instead I would recommend working with XFDF, and doing the XFDF to/from OData conversion outside of webviewer.
The XFDF spec is open, and we do follow it, with a few extensions, but these don't break XFDF compatbility. For example, we support Widget annotations, which are the visual aspect of PDF fields. We also add a <defmtx> entry, which maps the coordinate system of the XFDF annotations, into XPS coordinate system (which has a flipped y, and a different default dpi then PDF). You can ignore both of these in your conversions. The Xod file itself contains its own defmtx entries, so those will be used if none are found in the XFDF file.
If you are only dealing with certain annotations (such as text highlights) then you would not need to write a full XFDF/OData converter, and just worry about those particular entries.
If the above information doesn't help, then feel free to explain in more detail what you are doing (you can also contact support in this case, instead of this forum).
Also, note that there is a separate WebViewer forum. I will cross post this conversation there.https://groups.google.com/forum/#!forum/pdfnet-webviewer