If you're suffering from the problem "Synchronization only updates the
agendas.org file even though other files are added to index file" (
https://github.com/matburt/mobileorg-android/wiki/FAQ#Synchronization_only_updates_the_agendasorg_file_even_though_other_files_are_added_to_index_file) but the steps listed there don't fix the problem, I may have another solution for you.
The issue is that org-mobile-push has a bug where if the path held by the org-mobile-checksum-binary variable contains a space, every checksum that it performs on your org files will fail and your checksums.dat file won't list any of them. This affects all platforms but is especially likely to impact Windows users since "C:\Program Files" is where programs get installed by default.
I sent a patch to the org-mode maintainers that has been committed, so the next release of org-mode should fix the issue. In the meantime, you can work around the problem putting your checksum program in a directory that doesn't contain spaces. For instance, you can follow the directions in the FAQ, but make sure you install sha1sum to a directory that has no spaces anywhere in its path (e.g., put it in a folder called C:\checksum\ on Windows).
-jacob