I have always been saving my document in "Word 97-2003 Document (*.doc)" format.

I always save and edit in Outline view. Sometimes I have been tracking changes inside the doc (as well as via Subversion), and sometimes there are no tracked changes in the doc, and that feature is turned off inside Word.

I have been storing my revisions in a Subversion repository. This is convenient because it allows easy and arbitrary diff creation and viewing as well as labelling the different revisions. There is no compatibility problem inherent in storing the Word docs in Subversion, is there?

This morning, I saved some previous revisions to the file system on my hard drive, from the repository, using TortoiseSVN to retrieve them from the repository. There is one revision, r614, that loses its reference info as soon as it is modified in any way, including renaming it, including saving it to .docx format. I could send it to you. It starts off (as it comes out of Subversion) being 695KB, then shrinks to 165KB when any modification is made and the revised doc is saved. In contrast, r612, coming out of the repo, never has any problem; I can revise it a little bit in any way I have been able to think of, then save it, and all the links that were live seem to still be connected, clicking Zotero Refresh doesn't seem to cause any problems, and the size doesn't shrink as reported by Windows (file) Explorer.

The trouble is that after several times reverting back to that apparently uncorrupted version, then manually editing it to reinstate the changes I had made from r612 to r625, the resulting document always seems to develop the same loss-of-links-or-data problem. I have looked at various diffs to see which edits might be responsible, but I don't see any places where I edited part of a citation instead of correctly adding, removing, or replacing whole citations. So eventually I gave up and decided to seek professional help.

Looking back at older revisions (before r612) in my Subversion repo, I notice that the Zotero-generated bibliography has changed its font from Calibri 11 to Times New Roman 12. I believe I did not manually change it. I don't know if that is related.

I was worried about corrupted data in the doc going unnoticed for awhile, and then causing massive data loss later. It feels like that is what is going on. I have never been able to copy and paste a paragraph containing a citation, and have its citation survive as a link to reference-data. Sometimes I have been able to drag-and-drop paragraphs and the citation survives as a living link to a reference. Dragging-and-dropping in the Navigator Pane has never allowed citations to survive as other than dead characters that look correct but don't really link to any real reference in the bibliography or elsewhere. Is this the correct behavior?

I also just noticed that in r612 and earlier, the citations were stored in Bookmark format, and in the problematic, later versions they somehow changed to Fields. I did not change that in Zotero Set Doc Prefs|Format Using: , although I can see the change revealed there in that dialog box, when brought up from inside the later document versions. What does "Microsoft Word Fields are less likely to be accidentally modified" mean, BTW?

When I took one of the problematic revs (r614) of my doc, opened the Zotero Set Doc Prefs dialog and tried to change Format Using from Fields back to Bookmarks, I got the error message "[Exception... "Component returned failure code 0x80004005 (NS_ERROR_FAILURE) [zoteroIngerationField.getCode]" nsresult: "0x80004005 (NS_ERROR_FAILURE)" location: "JS frame :: chrome://zotero/content/xpcom/integration.js :: <TOP_LEVEL> :: LINE 1118" data: no]

I have just sent Report ID 1950596957 to Zotero with this message.

The other setting in (Zotero) Document Preferences is that I have been using my own Citation Style which should be almost identical to that I uploaded to the public .csl repo as Hypotheses in the Life Sciences (HyLS).

Thanks,
--Chris

I had suspected SVN/Tortoise myself, but tried and could not reproduce any problems by messing around with them. I was able to reproduce this problem by starting with r612 of my doc (from SVN's repo), then editing it without SVN/Tortoise for an hour or two.

Doing a diff on Word revisions with TortoiseSVN, opens the same kind of window with the same info, that is opened from within Word by clicking the Review tab in the ribbon, then clicking Compare and selecting "Compare...", then comparing two files. So I suspect any problem diff'ing, resides in Word.

So I don't know where the bug lies. Thanks for helping.

I have a question about Zotero Standalone. I have not been using ZOtero for a month or two now and when I reopened it today, many of my references seem to be gone. The motherboard on my other computer crashed in November and I may have saved many of the references when working on that computer. However, I thought that ZOtero automatically syncs. Does this have anything to do with two computers or is it due to something else?

Thank you for the answer. No the references aren't online either. I saved the data from my old computer though, is there a way to get the references from Zotero from that data? Is it saved somewhere? Thank you.