Yes, tx can definitely make gum disease worse. I don't know if that's true for everyone but I've read many posts here about gum and teeth issues on tx.
Since I already had periodontal disease I am used to having my teeth cleaned every 4 months. During tx my hygienist recommended that I have them cleaned every 3 months (or was it 2 months?), since the inflammation worsened during that time.
What's most important is very careful dental care: flossing daily, brushing often, and reducing mouth dryness in whatever way works for you. Through others here I learned about Biotene, which is available in toothpaste, mouthwash, and lozenges, for treating the dryness. This did help, for me. Even rinsing your mouth with water periodically will help.
Good luck to you, I know this is challenging in the midst of tx. The good news is that it should get better over time, once tx is finished, and if you continue to take very good care of your gums and teeth.
I had periodontal surgery in February. I do think treatment exacerbated some existing periodontal problems and I did not have the mouth dryness or mouth sores during treatment. I can't say treatment caused the gum disease but it certainly made it much worse. Must admit though, I didn't floss like I should have either.
Trinity