Will I Be Okay to Wait Until my Treatment is over to Get Cavities Filled, As my Orthodontist Says?

Because of feeling no pain,and b/c last dentist check up i had years ago came back clear,i went to ortho first.Got my digital images done and made payments.I decided to go to dentist while I wait for aligners to come in, to get a cleaning and come to find out i have 6 cavities apparently.my ortho says i can NOT get them filled until AFTER my treatment(which will be 14 months).I am really uneasy about this because i am afraid it will turn into a root canal by then.