Thanks everyone, hm's example is the closest to what I'm talking about, I suppose. It's not about allophones, there's plenty of these, think of all the nouns and verbs where you stress the first syllable in the noun but the latter in the verb.
It's really specific to the pronunciation of the vowel, and the meaning appears to stay the same. Another one I've just thought of is can:
e.g. I don't know I can. → /'cæn/
I can help. → /cən/
Again æ → ə. 'A schwa or a full vowel sound,' just as you say, hm. The vowel is somehow reduced to a laxer form or something like that. The word I'm looking for doesn't describe the words that exhibit this property but rather the process of vowel mutation as a feature of a language.