I understand layers exist but not fully how they work either. But I'm playing Brawl with ygra as my commander i have her on the field and the opponent cast fresh start on ygra. Which removes all of her abilities. Yet all the creatures on the field continue to remain food artifacts. Even new ones. The opponent rage quit soon after and I feel like i won due to a glitch? Using android on a galaxy tab.

There is nothing to fix here, this works as the rules dictate it does. Due to Ygra granting a card type (artifact), the effect starts applying in layer 4, long before the ability generating the effect is removed in layer 6. And due to rule 613.6, once an effect starts to apply, it will apply fully, no matter what, removal of the ability generating the effect in the process does not change that.