If I am using a Raspberry Pi 3 with Raspian as the software (Raspbian is a free operating system based on Debian optimized for the Raspberry Pi hardware. ... However, Raspbian is still under active development with an emphasis on improving the stability and performance of as many Debian packages as possible.) will the Debian-based version of FFS work?
TIA!
Raspberry PI - Debian
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If the officially-provided version was compiled on Intel x86_64, which I suspect it was (and you could verify by running file "file /usr/bin/FreeFileSync"), it will not execute on the ARM-based processors. You'll have to compile it yourself.