Thank you all.
Sorry, I meant "However, when searching in the EXPORT folder it only shows 15624 doc files."
Well... duplicate files? this is something new. I am only using Windows 8.1 (not linux). I see it mentioned somewhere else too, also regarding Calibre:
http://ask.metafilter.com/222066/Dup...he-same-folder
I think calibre (even if it's cross patform) should rename the duplicate files it would encounter when saving to disk - and it actually does: I have duplicates (same title and author, different ID) and when saving to disk they appear as file name (1).doc. So I shouldn't have duplicate files -unless maybe when the letter case is different - that would mean I could have FileName.doc and filename.doc in the same folder ...
I am counting the files in the EXPORT folder using Void Tools' "Everything Search" -maybe it is unable to count duplicate files as different files, I'm gonna check it out.
Another solution might be to save to disk using the {id} in the folder name, so even if two files would have the same name they should be in different folders. I will try that.
L.E.: Unforutnatelly I can exclude the duplicate files hypothesis. There are 31274 files in the export folder, including the opf files; there are 15624 doc files and 15627 opf files and 26 covers. The 31274 file count is reported both by windows (folder properties) and "everything search".
I can only assume Calibre is not exporting all my 15660 doc files - but the why isn't there any error message?