Download and install both TSmuxer and MKVMerge GUI (See Resources). Open TSmuxer and click the "Add" button at the top. A new window will appear. Select your MKV file. You will see the list of files inside the MKV.
Click the "Demux" button at the bottom of TSmuxer and click the "Browse" button. Select a place to save the files after they are taken out of the MKV. Click "OK" and "Start Demuxing" to complete the process.
Open MKVMerge GUI and click "Add" from the top. Select the files that were removed from the MKV in step two from the window that appears. Click "OK" and click "Start Muxing" to recreate the MKV files properly. When the process completes, the MKV file will be fixed and playable.