It shouldn't make your flare worse unless you have some type of adverse reaction to 5-ASAs which it doesn't sound like you do since you take it all the time and seem to be fine. I would never stop taking mine when in a flare.
25 years old; diagnosed March 2007;
Currently: persistent rectal inflammation
Asacol, 4 tabs, 3xday; Rowasa nightly; Viactiv; Metamucil wafers; multivitamin; Primadophilus Reuteri; sublingual allergy drops; Ortho Tri-Cyclen