I'm using Mendeley Desktop 1.9.1 on Mac OS 10.8.4. I wasn't aware of this happening in 1.8.x, and I would have done the exact same sequence of commands then. The 1.9.1 changelog also says "Fixed an issue where file attachments were lost locally after a sync if upload the attachment failed.", this sounds similar to what I'm experiencing, but not identical.
My issue is that Mendeley is unlinking attached local files on Sync. Note that I've not actually lost any data, due to the very sensible policy of not deleting files, but the data is unlinked from the metadata. Also, I don't actually synchronise files with Mendeley (i.e. "Synchronize attached files" is unchecked for my entire library), I only sync metadata.
I have the log file log-2013-07-16.txt (from --verbose-log), which covers Start-up, Case 1 and Case 2 below. Case 3 is from memory, as I didn't want to try and delete more files. Before creating this log I had Mendeley 'tidy up' unlinked files to reduce noise in the log (I kept backup copies obviously).
I can email the log if it will be helpful.
Start-up)
1) Open Mendeley (via Terminal.app so as I can add --verbose-log).
1A) Mendeley automatically syncs
2) Select 'Broken Sync' tag (I tagged at-issue entries for my own reference)
3) Manually hit 'Sync' button, just-in-case
Case 1)
Item is a web-page, it has a PDF file attached.
1) Add the HTML version to entry ('Add File...' in 'Details' section)
2) Wait for filetype icon in browser to change from PDF to multiple
3) Manually hit 'Sync' button
Result: The HTML document gets forgotten, which I would not expect.
Case 2)
Item is a paper, it has no files attached.
1) Add the PDF file to the entry ('Add File...' in 'Details' section)
2) Wait for PDF filetype icon to appear in browser
3) Manually hit 'Sync' button
Result: The PDF document gets forgotten, which I would not expect.
Case 3 -- not in log as I do not wish to unlink more files)
1) While investigating disappearing file notice that another web-page is misnamed, HTML and PDF versions have been attached for months
2) Correct title of entry
3) Manually hit 'Sync' button
Result: The HTML and PDF versions are both forgotten, despite being attached for months! Definitely not what I would expect.
If you require more information (or the log file) then please let me know.
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