Change the transfer mode from Auto to Binary and all file types will be transferred AS-IS without any alterations.
This can be done for the current session via the main menu > Session > Transfer Mode > Binary
Or if you want to default to Binary mode from now on when you start FlashFXP then via the main menu > Options > Preferences > Transfer > Transfer Mode > Binary and Click OK to save the changes.
(This does apply the new Transfer Mode for the current session)
The ASCII text file conversion is done on the server-side and sometime the result is not what you'd expect.
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