I have not seen these specific issues. Would it be possible to detail a little more about the size of the design you are migrating & the results that you are seeing?
25 pages w/ 3 levels of hierarchy
OATS in the existing design are used primarily for 4 reuse blocks
In the migration process REFDES OATS values are migrated but the XYZ values are not
The xref attributes do not come over at all
Hopefully with a little more insight to your environment this forum can help you a little better.