It may be obvious, but let me ask anyway: if I download all presets from my TF to FactorLib and then save that .syx file to hard disk, am I actually making a backup of these presets? In other words, if I later upload that .syx file to my TF, will it overwrite all the changes I have made in the meantime and return everything in original stage?
Yes, the .syx file will be a backup of your presets. You can save an unlimited number of .syx files to your computer with different sounds in each one. This way you could in theory build a library of thousands of Factor pedal presets on your hard drive.
When you send a .syx file back into the Factor pedal it will overwrite the internal presets.