Of course you can use a Harmony remote with Ignite. Did you really expect the installer to reprogram your Harmony remote? When you get a new TV, a different brand, you have to reprogram the remote. This situation is the same, but what is crazy is that you expected something different.
Switching to Ignite was a good idea, and you may still want to do that when in the future. Unfortunately, you have started down a dangerous path that potentially has some snags. Hopefully you will get your phone line restored with the original telephone number shortly.
If you do switch to Ignite and need online assistance with reprogramming the Harmony remote just post a note. There is lots of experience and help available.