I've done a good bit of this with Music and a little bit with movies. You need to do kind of an odd sequence to make it work correctly. Here's an outline of the process:
1. Rename your existing file (the one you want to get rid of) using the RM&C command in MC. Make the new filename something REALLY simple like "a.avi". In your case, since you are changing formats too, let's go ahead and rename it to "a.mkv". Again, use the RM&C tool to do this. You will probably need to use the Find and Replace template in order to change the extension to mkv.
2. Name your new file (the one you want to keep) the exact same name. So rename your new MKV file to a.mkv . Use Windows Explorer or another file based tool to do this.
3. Copy the new file over the top of the old file, replacing it. Also use Windows Explorer or another file based tool to do this.
4. Now MC should see your new file with the really short name (a.mkv), but it doesn't know it's got new stuff in it yet. So, update MC so it sees the new stuff.
<right click on file in MC> Library Tools > Update Library (from tags)
This will force MC to re-read the file, and bring in it's new format, duration, etc.
5. Rename the file, using RM&C back to a name that makes sense. I generally use the [Name] and [Year] fields, as this is enough info for me in the filename. However, I see that your names have more detail in them. If you want to keep that detailed name, then you will need to either manually re-type it (in RM&C) or copy that filename to somewhere else before you start and then cut and paste it into RM&C.
Other than step 5, this is actually a lot faster and easier than it sounds. But it is detailed and you have to keep track of what you are doing.
Good luck,
Brian.