I'm not quite sure what you're referring to; Are you importing commands from these .vap profiles?
When do you see an "UNABLE TO EXECUTE..." message?
If you import and overwrite a command that is executed by another command, getting an "UNABLE TO EXECUTE COMMAND. COMMAND NOT AVAILABLE." message is normal.
Commands are identified in two different ways: By their command phrase(E.G. "Command 1"), and their internal GUID(a long string of character serving as a globally unique identifier).
When you speak a phrase, a command is executed by matching the command phrase assigned to it. However, if you use the "Execute Another Command" action, the target command is instead matched by the GUID. When you import commands, that GUID will have changed, and no longer match.
If you frequently overwrite commands, you may want to use the "Execute by name (Advanced)" option of the "Execute Another Command" action instead, as that does use the command phrase(or part of it), rather than the GUID. Note that this option is marked "Advanced" for a reason, so use with caution.