More Awesome Than You!

I deleted Lord Darcy's higher comfort and energy for beds/tubs (put in where it told you to put it) and when I loaded the game, it said that Pets was uninstalled, and that all pets would be deleted.

I once had a similar problem with Uni thinking it uninstalled itself.
I quit before the game could delete my campus/YAs, and then ran a defrag, and after that, my game loaded as normal, Uni included.
I really don't know why it happened, or why a defrag fixed it, but it wouldn't hurt for you to try that if no one offers any better ideas.

Check the registry is still pointing to the correct folder for Pets. Try re-installing Pets back over the top. If it still says you don't have pets, run your defragging program and find out that you were 95% fragmented and 50% corrupted because the scheduled nightly defrag hadn't been running for months, then re-install the offending EP again and all will be well. (If you reinstall an EP that you're not running from, you don't need to do any .exe-replacing, but if you use clean templates for that EP you need to put them back in :)) Good luck!

Okay then, I think I'll reinstall pets and see what that does, hopefully that should solve the problem.

This happened to me once with OFB.  It turned out that my .exe file had been deleted.  Make sure that you still have Sims2EP4.exe installed in the following folder:

Program Files/EA Games/The Sims 2 Pets/TSBin

If it's missing, you can just copy it off the installation disc.