I've posted a couple times about this issue.
Currently, I am using 3 Primes with Tvheadend with a simply patched version of Tvheadend's native HDHomeRun support. It works like this: change the network type of your tuners to ATSC-C, and create an ATSC-C Network. Then, when creating muxes, instead of using the actual frequency that the channel is broadcast on, use the cable/virtual channel number as the mux. Each mux will have only a single service, which corresponds to the stream from that virtual channel. When tuning, my patches version of the Tvhdhomerun adapter will tune the vchannel and handle the stream decryption.
I've used this with both the 4.2 stable branch, and am currently running this patch with 4.3/master.
(I am currently also working on a larger patch-set that adds proper CableCARD/Prime support to Tvheadend, but haven't had much time to work on it recently.)