For this situation I would highly recommend that you make sure that the global setting that X3 is referring to in the preferences is checked.
From the main menu, Options > Preferences
Then from the Preferences dialog under Connection / Folder caching
[x] Refresh on file transfer
This will ensure that no files are missed, now depending on the situation if the user uploading the files is uploading the files while you are downloading its possible that some files might be missed, in which case you'll want to wait until the person uploading has indicated that all files are uploaded.
You can also clear the cache at any time within FlashFXP from the main menu, Directory > Clear folder cache
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