I am running a SWTOR based F&D game.

It hasn't come up yet but some Force Powers have a light side and a dark side expenditure option. What would happen say a Jedi wanted to Heal someone with Heal/Harm but only rolled a dark side pip. Would they be able to gain a stress and conflict and flip a destiny point to turn the pip from dark to light or would they still only have the dark side option of Heal/Harm?

I cannot get clarity from the rules so far. It simply assumes no one would desire this.

Any thoughts?

The rules show the standard force die pip symbol of half white and half black in both of the Heal/Harm basic abilities. This always means you can convert pips unless the power explicitly says you must spend light or dark pips only.

Basically, always assume the normal rules apply unless the power explicitly tells you otherwise.

The only restriction is that a character that has fallen to the darkside cannot use the lightside ability, as it specifically calls out.

It might seem weird to use the Dark Side to heal someone, but remember that the Dark Side is fueled by any strong emotion, not necessarily negative emotion. So you see your beloved friend shot down by blaster fire and rush to his side. You try to remember your training to remain calm as you heal him, but it just won't come. Mechanics-wise, you rolled a bunch of Dark pips, but narratively, you are filled with love for your friend, fear of losing him, and anger at your helplessness. You use that surge of emotion to draw your friend from the brink of death. You are exhausted (strain), but your friend lives. You embrace, and your path down the Dark Side begins with the very best of intentions...

Doesn't a light side Jedi have to use a Destiny point to use dark side pips, and vice versa?

The only time I think you are actually proscribed in how you use force pips (rather than just what you need to do to be able to activate them) is with the Influence power, where calming or positive emotions need light sided pips, while aggressive or upsetting emotions need dark side pips. I don't remember there being a specific mention of the colour of pips for Heal/harm, just requirements for being lightside or dark side users, which is determined by morality, not the pips of the dice.