The usual version of this message rel;aes to large image import, which does not appear to apply.
http://helpx.adobe.com/encore/kb/error-software-used-decode-media.html
What method did you use to import the new footage? Replace asset? delete and replace? add the new footage to the old?
Do you still have the original m2v to import as a test?
I assume you are using Encore CS6, true?
PC or Mac? OS version?