Hi Naira (Nicole?),
I'll start with the second question: the limitation on 4000 hits is not a fixed one. What matters is how big the single import is after EPPI-Reviewer has digested it on your side; if the references have long abstracts, or happen to have a lot of comments, the total import size will be bigger than usual and it is is entirely possible that 3565 references may end up producing a too big single import. Also, the actual communication uses compression and what counts is the size after the compression, making it (even theoretically) impossible to estimate in advance when an import will fail. This is a sore point for us (significantly reduces the user-friendliness of EPPI-Reviewer) but unfortunately I have been unable to design a better mechanism (for now). For you, this means that you will need to cut the third file in two smaller fragments, I'm afraid.
As per re-unifying the sources after the import, the only way to do this is to use dedicated codes to group items per source: you could create a (single-user) code-set called "Sources" with a range of selectable codes, one per actual source (EMBASE, PsycINFO , etc.). From the Sources tab (lower left corner in the main screen) you'll be able to list all items in each source (you may also want to raise the number of items shown in one page to 4000, this is done through the "select the fields to display" button in the main Documents toolbar), select all items from one source, right click the corresponding code and and "assign selected items to this code". Do the same for all sources, and the problem should be solved. This will also allow you to create the flow charts directly from the "Diagrams" tab in EPPI-Reviewer.
One more advice: the procedure above should be done after completing the Duplicate Checking. The "Automatically mark" procedure is designed to ignore already coded items (to avoid marking as a duplicate an item that has been already coded in meaningful ways), so it is better to leave the items uncoded until after dealing with duplicates. This issue can be side-stepped by setting an appropriate threshold via "Advanced Mark automatically" so it isn't a strict requirement; still, a little caution does help.
I hope this will allow you to overcome the current obstacle.
Best wishes,
Sergio