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Not sure why you were getting so many files. It sounds as though you did something that made DropBox think all the files had changed. The stats in the calibre2opds log will tell you exactly how many files were changed in that particular run - and that is the number that DropBox should sync as a result of that run. In fact the Minimize Changes options was added specifically to help DropBox users and it certainly seems to work fine for me. I wonder if you did a run WITHOUT the Minimize Changes option set - that could have the sort of effect you describe. With the 2.4 release onwards there is also the synclog file generated in the calibre2opds log folder which should give you an exact list of the files that were copied (or not copied) to the new catalog (and thus need syncing). Looking at that might give an indication of what is happening.
If you are using the 2.5 beta 1 release then you may want to also use the feature that has been added to reuse the calibre cover.jpg files for thumbnails and cover images rather than generating new images optimised for that purpose. This means there are less files stored in the library thus saving some space (although there is more network trafic when browsing a library as the cover.jpg files are normally larger than the optimised images that calibre2opds would otherwise generate).
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