When MobileOrg synchronizes with the server, it not only pulls the Org files for viewing. It also appends captured entries and pointers to flagged and changed entries to the file mobileorg.org on the server. Org has a pull operation that integrates this information into an inbox file and operates on the pointers to flagged entries. Here is how it works:
org-mobile-inbox-for-pull. Each captured entry and each editing event will be a top-level entry in the inbox file.
:FLAGGED:, so that they can be easily found again. When there is a problem finding an entry or applying the change, the pointer entry will remain in the inbox and will be marked with an error message. You need to later resolve these issues by hand.
:FLAGGED:tag along with the recorded flagging note (which is stored in a property). In this way you indicate that the intended processing for this flagged entry is finished.
If you are not able to process all flagged entries directly, you can always return to this agenda view2 using C-c a ?.
 mobileorg.org will be empty after this operation.
 Note, however, that there is a subtle difference. The view created automatically by M-x org-mobile-pull <RET> is guaranteed to search all files that have been addressed by the last pull. This might include a file that is not currently in your list of agenda files. If you later use C-c a ? to regenerate the view, only the current agenda files will be searched.