To me, it seems perfectly obvious that it is better to keep CMANO around.
CMANO isn't hurting anything, and it is a clean version with no known bugs. In fact, CMANO can also serve as a benchmark to remind game players how COMMAND used to play BEFORE CMO came on the scene. The two games are easily compared using this method. So, if things don't appear to be working properly or the same in CMO, you have a point of reference (CMANO) as to how they used to work and that can be quickly pointed out.
As the other poster noted, CMANO also serves as a platform for playing any of the older scenarios that don't quite seem the same when being run on CMO. (You created many of these older scenarios, so I'm sure that you are in favor of being able to keep a means to be able to play them the way that you intended them to be played.) For example, air strikes which were formulated in CMANO have been altered due to the new flying logic in CMO, and that significantly changes range distance, and attack profiles for these older scenarios (like yours).
Finally, CMANO is a means of being able to convert really old scenarios up to version 478 before they are later converted to CMO.
I see no known problem with keeping both, all the time knowing that CMANO will no longer be supported. Who knows, as CMO cuts its teeth, perhaps keeping CMANO might be a really beneficial for foreseeable future.
I'm keeping (and using) CMANO for those reasons. Unless you are strapped for HD space, keeping CMANO around for a while seems like a no-brainer to me.