Harry,

so i was wondering what advantages it could give me to make a ffp
file, because there is already a internally stored md5 checksum on the
decoded audio data inside the flac file?

Testing the .flac file against its internally stored fingerprint lets you know that you have a properly encoded .flac file of *something*. If you also certify that internally stored fingerprint against a list of correct fingerprints in another file, then you know you have a properly encoded .flac file of the *right* audio, and that the person who sent you the .flac files didn't accidentally provide a wrong file instead.

Yes, a miscreant who would intentionally switch .flac files on you would also alter the .ffp file to show the fingerprint of the wrong file instead of the right one, but that could not happen by accident. Sending a set of .flac files with an .ffp file says, "I wouldn't deliberately deceive you"; sending a set of .flac files with no checksums at all says "I never make mistakes." There are people whom I'd trust not to deceive me deliberately but nobody from whom I'd accept a claim of infallibility.

Moreover, if a set of .flac files is being shared, a copy of the fingerprints can be kept at a URL distributed with them, so that everyone receiving them can make sure that the fingerprints of the files (s)he gets match those of the original set.

i was also wondering how files encoded by using the new
--keep-existing-metadata option are verified when using -verify. Is
there a separate internally stored md5 for metadata next to the md5
for decoded audio data or how is everything verified?

Until we hear from someone who knows, I'd venture to say that --verify does just what it always did, and it has nothing to do with existing metadata in the uncompressed input. As it encodes each segment of the audio, it re-decodes it and compare the result to the original input.

Is making a ffp file for such files also possible for the non-audio
data (so all metadata)?

No, fingerprints are defined only for audio.

i was also wondering if there exists a GUI program for win32 to verify
flac files using a ffp file (so not md5check.exe)

Yes: Trader's Little Helper at http://thor.prohosting.com/roh0205/.

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