Does that mean some stations will no longer be able to broadcast in HD? I mean, if say WPWR were to move to a subchannel of another station, they wouldn't be able to broadcast in HD, right?
No. Equipment exists right now for TV stations to run dual HD originating from 1 signal, with excellent picture quality on both sub-channels.
Presently Channel 60 WXFT-DT has 2 HD channels at 1080i, plus 1 SD channel 480i. Channel 7 WLS-TV has 2 HD channels at 720p, and 1 SD channel 480i. Channel 56 WYIN has 2 HD channels: 1 at 1080i and 1 at 720p. Last year Channel 9 WGN-TV tested a 2nd HD channel with both at 1080i, plus 2 SD channels 480i.
Some stations will need to buy new equipment in order to transmit dual HD. I suspect that some sub-channel diginets will be eliminated when everything gets completed. Some diginets won't make the move to the new channel due to lack of bandwidth. Also, there won't be enough room for diginets that are already airing on a station that is getting a new primary channel moving in.
When ATSC 3.0 becomes the new standard, I heard much much more video can be compressed. When that happens (5-10 years from now), Chicago can get back to the same amount of programming choices it has now, plus more.