You cannot make sure that your game will not trigger seizures, ever, since the thresholds differ by orders of magnitudes between individuals and beetween the same person on different days and under influence of a hundred other factors which you cannot know about (lighting conditions, distance to the display, sleep deprivation, stress level, background noise, alcohol intake, etc).
If you can, that is if it doesn't disturb the game's look and feel, you may try as jokoon said, reduce the flashing a bit. If that would "destroy" the game's look and feel, scratch the idea.
Regardless, if you see a reasonable possibility that your game might trigger epileptic fits, you should add a (loosely worded) warning somewhere on the download page or on the package.
Something like "Note: This game contains vivid graphics. Video games (in general) may cause...". This will give people who have a known seizure disorder a valuable hint, and that is as much as you can do -- for them, and for yourself.
You cannot prevent people from having seizures, but you can prevent them from filing a lawsuit against you claiming that you didn't warn them.
I would however avoid saying "This video game may cause..." because that would be
a) massively negative marketing and
b) possibly the opposite effect of what a disclaimer should achieve (one could argue: "Hey wait, you knew this game was designed in a dangerous way and you still sold it?")