In the event someone else runs across this issue, I found the answer on FabFilter's forum. Someone asked the following:
Q: Sidechaining in Reaper is normally done by increasing the channel count of a track. In the case of a regular stereo signal, this would be a change from 2 to 4 channels.
Unfortunately, Pro Q3 switches the plugin from Stereo to Quadro Mode when there are more than 2 channels on a track. The processing of channels 3/4 is also activated by default which can be confusing when tracks 3/4 are used later.
Is there a way to use the sidechain in REAPER while keeping Pro-Q3 in stereo mode?
A: Yes! In recent Reaper versions, there's an option for this. In the plug-in connector, click on I/O, then set "Request VST3 bus channel count" to Stereo.
https://www.fabfilter.com/forum/3423...eaper#comment0