If there is a cantillation that is a stop (like etnachta, revii, zakaif katone, pashta, etc) on the word that ends with Havara Petucha, then that cantillation stops the effect of the Havara Petucha.
Which is an explanation of why we generally sat “borei p’ri hagafen” although “borei” is havara pesuchah (ends with aleph) – apparently, tere’s supposed to be a pause between “borei” and “p’ri” (some do actually sat “f’ri”).
(I got my information from dailyhalacha.com, I’m no dikduk expert).