Data from a Linux filessystem will loose all its Linux features as ownership, permissions and links. It is also problematic when having long filenames.

Therefore if possible do not use FAT.

Even having the same filesystem, some copy commands exclude dangling symlinks (symbolic links that point to something that does not exist).

diff -ru <dir1><dir2> will show that.

Dangling symlinks are errors and therefore something to be fixed before doing the backup. find . -type l -xtype l -ls will show them

To have a very long lifetime use M Discs and a M Disc capable burner.

CD, DVD, Blueray have their own filesystems and features.

Applications as k3b have options for Linux and symlinks