Some Betta's just don't have enough stimulus to flare and thus won't until some comes into play like a mirror or another Betta or he see's his reflection.
And don't worry, usually sucking them up doesn't hurt them, I've done this to my girls many times as well as some of my cories >< lol but they're all fine, just push him out of the way is all. But I guess if you're more comfortable with taking him out then continue doing it.
Okay so for now, i suggest you do twice weekly changes at 50% on one day and 25% at the end or visa versa. This will keep the water clean and help him regrow his fins back and also take out most threats of fin rot. Use Stress Coat at double dose if you have it/can find it and he should be set