rsync --delete --files-from=list / dest/ does not delete unwanted files

Perhaps you could do this using a list of include patterns instead, and use --delete-excluded (which does as the name suggests)? Something like:

rsync -r --include-from=<patternlistfile> --exclude=* --delete-excluded / dest/

If filenames are likely to contain wildcard characters (*, ? and [) then you may need to modify the Python to escape them:

re.sub("([[*?])", r"\\\1", "abc[def*ghi?klm")

Edit: Pattern-based matching works slightly differently to --files-from in that rsync won't recurse into directories that match the exclude pattern, for reasons of efficiency. So if your files are in /some/dir and /some/other/dir then your pattern file needs to look like:

/some/
/some/dir/
/some/dir/file1
/some/dir/file2
/some/other/
/some/other/dir/
/some/other/dir/file3
...

Alternatively, if all files are in the same directory then you could rewrite the command slightly:

rsync -r --include-from=<patternlistfile> --exclude=* --delete-excluded /some/dir/ dest/

and then your patterns become:

/file1
/file2

Edit: Thinking about it, you could include all directories with one pattern:

/**/

but then you'd end up with the entire directory tree in dest/ which probably isn't what you want. But combining it with -m (which prunes empty directories) should solve that - so the command ends up something like:

rsync -m -r --delete-excluded --include-from=<patternfile> --exclude=* / dest/

and the pattern file:

/**/
/some/dir/file1
/some/other/dir/file3

As you explained, the command

rsync -r --delete --files-from=$FILELIST user@server:/ $DEST/

does not delete content in the destination when an entry from $FILELIST has been removed. A simple solution is to use instead the following.

mkdir -p $DEST
rm -rf $TEMP
rsync -r --link-dest=$DEST --files-from=$FILELIST user@server:/ $TEMP/
rm -r $DEST
mv $TEMP $DEST

This instructs rsync to use an empty destination. Files that are already present in the link-dest-directory are locally hard-linked and not copied. Finally the old destination is replaced by the new one. The first mkdir creates an empty $DEST if $DEST doesn't exist, to prevent rsync error. (The $-variables are assumed to carry the full path to the respective file or directory.)

There is some minor overhead for the hard-linking, but you don't need to mess with complex include/exclude-strategies.

Inspired from m4t, but using ... rsync for cleanup

rsync -r --link-dest=$dest --files-from=filelist.txt user@server:$source/ $temp
rsync -ra --delete --link-dest=$temp $temp/ $dest

This is not exactly the solution, but people coming here might find this useful: Since rsync 3.1.0 there is a --delete-missing-args parameter which deletes files in the destination directory when you sync two directories using --files-from. You would need to specify the deleted files in /tmp/list along with files you do want copied:

rsync --delete-missing-args --files-from=/tmp/list /source/dir /destination/dir

See the man page for more details.