These conservation laws apply to open systems (which biological platforms are). All ready at the cell level the primary concern is how to "efficiently" do energy cascades which sometimes have unintended (irreversible) side-effects. So cells get "garbage collected", there are other more system level irreversible changes, some intended (memory) and unintended, which I guess are indeed ultimately unsalvageable, which is why reproduction is a thing (pristine copy of genome in new cell).