John
The OP is talking about copy protection not just copyright. Maybe I am misunderstanding. Also removing a copyright notice may be illegal.
Yes, but there can't be any copy protection without a way to first indicate in the file itself that it's protected, and the copyright notice is the only mechanism for doing so. There cannot be any copy protection in a MIDI file because it's a container of data, not an executable. It's entirely up to the software that reads that file to enforce any restrictions.
Which is apparently what SONAR thinks it's doing, although it's bizarre that the OP can't load back in his own file. That's why I suggested examining the data in the file to see if the copyright message originated with SONAR or if it was added by the Fantom.
As for the legality of removing a copyright notice from a MIDI file, it would have no bearing at all on whether the file was in fact copyrighted. It's copyrighted because it was registered with the USCO, and flipping two bits in the file doesn't change that. If I rip a song from a CD and turn it into an MP3 or WMA it's still copyrighted material even though I have substantially modified the data.
Now, if the OP had gotten this file off the net and it was copyrighted, then I'd have no sympathy for his plight. However, it sounded to me like the MIDI sequence was his own creation. SONAR did not complain when it was originally imported, and the problem only occurred when he reloaded it after using an external editor on it.