She for sure needs to be checked out by a vet again. She's likely to have something medically wrong with her if this is a sudden thing. Some things, like closed pyometras are not only hard to detect, but life threatening. And spaying would be the cure in that case.
If she still checks out fine, you might want to start treating her like a puppy and house train her all over again. Techniques like tethering can be useful in training.
As for the spaying, it's a good idea. It will prevent pyometra and other medical problems. Pregnancy can have health consequences as well--and you may be seeing the effects of that as well.
So all I can advise is that you have the vet take another look and have a discussion with him about the benefits of spaying.
Good luck, and keep us posted!
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