I’m not sure I understand your question—it does not seem to really relate to Synology or backups.
If you have files in a sparsebundle and back up the sparsebundle, any changes that you make will be reflected in the next backup. For example, if you remove some files from the sparsebundle, back it up again, and then restore it, the restored sparsebundle will not show the deleted files. In other words, you can back up a sparsebundle like any other folder. Just make sure that it’s unmounted to ensure a consistent copy.
If you are looking at the band files that comprise the sparsebundle’s storage, those will normally not get deleted (from the original sparsebundle, and therefore not from the backup either) when you delete files from the sparsebundle. Instead, that space is marked as available for other files that you may add to the sparsebundle later. (This is also true for read-write .dmg files except that there’s in effect a single band.) If you want the “unused” band files to be deleted to save disk space, you could compact the sparsebundle. However, this will not necessarily save space on your backup because rearranging the contents of the other band files could mark them as modified. You could end up with fewer total band files but more files that have changed.