If you don't already use tons of CEP content in areas/creatures/objects, then it shouldn't be a problem to remove it from your module. If you have already used content from it, you'd first have to edit every blueprint you've already made with it to use default appearances, then update any already placed objects (creatures, placeables, etc.), get rid of any areas built with any CEP-included (or -modified) tilesets, and otherwise remove any traces of CEP content before removing the haks.
While it has been a long time since the CEP was updated with version 2.4...I will be releasing version 2.60 sometime before Sept. 8th of this year.
I use a combination of CEP & Project Q (& a bunch of my own stuff). It's a lot of 2da editing, some minor file copying+renaming (for the few models that share a filename between the two projects but are different), and bookkeeping. But it can be done.
If you're already heavily invested into the build of your module and don't want the work of removing everything that used CEP, a merge might be your best bet as far as time goes. You wouldn't have to change everything you've already put in, and you could work the Project Q content in at the same time. I know a lot of people have the CEP and Project Q already downloaded, so a "merge hak" would be relatively small to add to what they already have.
My own opinion is use both to get the best of both worlds, but it takes time to get the content from both to mesh (and requires at least 2da updating every time either major project does an update to account for new and updated 2da entries).