The Helix will respond ONLY to those CC messages that it knows about. If you send a CC message that it does NOT know about, then it can do nothing with it, and will disregard it. Also, check re channels. CC messages are sent on a specific channel, the Helix may receive messages on certain channels ONLY.
There are certainly 'spare' Controllers that could be used, for example 'General Purpose' controllers. Some extra box could receive your data stream, and pass data on, but if any special controllers were seen then this data could be replaced/expanded into the extra functions you required. Of course this would make your setup more complicated. There may be something available, or you might program a laptop to do the job. It's a sort of reverse 'filter' job - a normal filter would remove certain data, you need to replace certain data. Look for 'filter replace midi data' or something like that?
Geoff