Editing EXIF with external editor from Elements 10 Organizer

Hello there.
I'm experiencing a kind problem.
I'm editing exif gps coord with external program.
Organizer config set to "Edit with GPSView", where GPSView is external GPS coords setter.
I'm setting the coords, the edited file copies itself, so, I have 2 files - with old GPS, and new GPS.
Then, I'm making "Flatten version set" - and then I have 1 file, with new GPS.
After that, when I'm tryin to edit same file's GPS once again, Elements turning GPS values to old values, which were before any exif edit. 
What am I doing wrong?
I have a bunch of files to edit GPS, and its really breaking me - it is unable to edit even GPS with these  "Elements".
Please, help.

Just a suggestion as I am not using GPS tagging : did you try the option to 'write metadata to file' (shortcut Ctrl W) after flattening the version set ? Does it make any difference?

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