It sounds like you have everything set correctly.
If you open the active edits window (from the FlashFXP window menu > View > Active Edits) does it show the file in the active edits list?
What type of storage is the local file on? hdd, removable drive, network drive, etc?
Quote:
In fact, the "save and upload" works only for remote files 
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The save and upload feature is specifically designed to work for local files, that fact that doesn't work for you has me rather puzzled.