yes, MultiAVCHD is a brilliant free program. If you are worried about quality loss due to transcoding then i would suggest using 2 pass VHQ as the transcode settings. It does take a long time but the results are a lot better than 1 pass turbo. It takes me about 12 hours to do a 2 hour movie using this setting (but this was converting a lagarith encoded avi to AVCHD so it should be quicker with a mkv)

Version 4.1 though has some player compatibility problems which wasn't present in version 3 so best to make a quick test to see if your player can play the files first