If I understand correctly, you could try this.
In the search window, make sure that "regex" and "current file" are selected.
Search for:
<p class="calibre2"><sup class="calibre3">(.*?)</sup>
Replace with:
<p id="id_v300100\1" class="calibre1"><sup class="calibre2">\1</sup>
Run this for chapter 1.
Change id_v3001 to "id_v3002" in the replace string.
Run this for chapter 2.
etc.
With the info you provided I don't see any alternative but to run this once for each chapter.
I haven't tested this, but it should work.