I am writing my thesis and it is almost complete but have started to have trouble with captions and cross-referencing that have been working fine all year. There are several issues.
a) captions appear in text and seem to be fine BUT are not present in the table of contents, nor the document map, nor in the list for cross-references. It is not consistent across all three, so figure 13 for instance might appear in one or the other. Yes, I have updated everything (entire fields etc) and yes, I have tried reinserting - neither of which work. It is the same for both Figures and Tables.
b) If I delete a caption (in utter frustration and resolved to try again) it works sometimes. However, in other places I am left with a blue frame which, when I try to delete it, gives me the message 'The section is marked as deleted text'.
c) cross-references that have worked in the past are now disappearing from the cross-reference list, and this morning, all my tables in the cross-reference list appear as doubles. So it looks like


Table 1 xyz
Table 1 xyz
Table 3 abc
Table 3 abce