I started an IF schedule where I eat from 4pm until 8pm a few months ago. I did have acid reflux issues in the beginning, but that stopped after a couple of weeks. In my experience, the acid reflux is worse if you eat shortly before going to bed. (In the beginning I ate until 9pm and went to bed at 10pm. Now I'm eating from 5pm to about 6:30 and go to bed at 10, with no problems. (I've had a sore throat for the last 4 years or so, but other than the acid reflux thing when I started IF, this has pretty much remained unchanged, so I'm assuming the intermittent fasting isn't making it better or worse.))

So you could try taking a ≈2h break before going to bed (if you're not doing that already), eating twice a day, experimenting with different foods, talking to a doctor, and if you still feel bad after that, I would suggest going back to a regular diet. Three months seems like enough time for the body to adjust as much as it's ever going to.