When I send my document to the printer all references disappear and the text reads “Error Reference Source Not Found”.

What can I do to print the document properly?

[Answer]:

What kind of references are these?

If they are REF fields (use Alt-f9 to look and you will see things that look like { REF myref } or { myref }, then it sounds as if all the bookmarks they point to have been removed. If so, it may be worth finding out why, but for the moment the following might work:
a. select the document body (e.g. ctrl-A)
b. press ctrl-F11 to lock all the field codes
c. print some pages to ensure that the error messages do not appear, and that things such as page numbers still work as intended.
d. If OK, print the whole thing.