How Do You Highlight or Find Specific Cross-reference For Endnotes in the Document?

To do this, you need to open the "Advanced Find" dialog. You can do this by opening the Navigation pane (to the Search tab) using Ctrl+F, then click on the tiny arrow beside the "Search Document" box, and choose Advanced Find..., but I find it easier to avoid the Navigation pane altogether, pressing Ctrl+H to open the Replace dialog and then selecting the Find tab.

Either way, once you've got the Find dialog open, you're going to use Find In, which will select all instances of the "Find what" item in a given document story (you'll have to select Main Document or Endnotes; you can't do both at once).

You can then search for endnote reference marks using ^e, or you can search for superscripted text by leaving the "Find what" box empty and pressing Ctrl+Shift+= (that is, Ctrl+Plus Sign). If you want to limit the selection to numbers, you'll have to use wildcards and search for [0-9] (formatted as superscript).

If you have field codes displayed, you can search for ^19 REF or ^d REF (both ^19 and ^d represent the opening field brace). This will find cross-references (unless they are PAGEREF fields).

The easiest way is to use CTRL+A and then F9 to update the fields in the document.  In that the cross referenced Endnote has been deleted, the cross  reference fields will display

Error! Bookmark not defined.

You can use the Replace utility to find that and replacing it with nothing.