[Mosu]

The differences are indeed only in a very small number of elements, and those should always have the same size. Therefore syncing the two files should be nearly trivial. I cannot tell the actual elements off-hand, but they should be the various UID elements (track UID, segment UID, tag/edition/chapter/attachment UIDs), the muxing timestamp ("Date:" in mkvinfo's output), and (if you have two different sets of mkvmerge executables) the "writing app" element.

The position of these elements varies: most of them are located at the start of the file before the first cluster (track/segment/chapter UIDs, muxing timestamp, writing app). Others can be at the end of the file because mkvmerge puts them there (tag/edition/attachment UIDs).

There are two sync tools I use regularly: rsync and unison. rsync is mostly a "from point A to point B" tool, and unison is a "keep two directory structures in sync and resolve differences" tool. Therefore rsync is better suited for this particular purpose. Both are available for various Linux/Unixy systems as well as for Windows, but my experience with them on Windows hasn't been that great. However, both run over ssh and only update those parts of a file that has actually changed making them incredibly efficient for huge files with small differences.