I'm creating a language where the stress is on the third to last syllable and I have a sound change where an unstressed short vowel at the beginning of a word is deleted. (so in 'a.ta.ra. the word vs (a)'ta.ra.ra. where the first vowel would be deleted) My entire language so far hinges on this sound change to be a thing please help?
This is really one of those times where the only viable answer is "it's completely up to you!"
Sometimes the stress changes, sometimes it doesn't. This depends on the stress rules of the language. In your case, I'd suggest that if you like that vowel deletion, then you should codify the rule to indicate that addition of a suffix that causes a shift of stress will also cause the deletion of unstressed short vowels.
If you don't address the rules regarding stress, then you'd leave yourself open to words like atárara remaining in the language.
This could give you some interesting consonant clusters word intially: tálipo > *talípora > tlípura. Nothing unusual there, really.