Hi,
According to your description, many table captions disappeared in the Cross-reference dialog when you crossed reference several table captions.
In order to help you with the problem more efficiently, I need to clarify the below information:
Did you choose the right Reference type (Table) when you cross reference?

The renumbering tables might cause the tables to be deleted.
We could recreate a new table caption then insert a new cross-reference.
Make sure you choose the right format when you numbering the tables:

Hope this helps.
Regards
Steve Fan
TechNet Community Support
