A 400-page CD set is normal. Estimating from all 400 at once is not — pick your sheets before the document even opens.
When you open a PDF of 25 pages or more through the desktop app’s Open PDF button (File → Open), Groundwork Takeoff pauses before loading it and shows the page picker: a thumbnail grid of every sheet, each labeled with its page number and detected sheet size (ARCH D · 24×36 in and the other common ARCH/ANSI/ISO sheets — it reads the paper, not the file name).
Use the All / None buttons to select in bulk, then untick the exceptions. Previews render in the background for the first 200 pages; every page stays selectable regardless.
This matters: the extracted sheets are a new, independent document — their own file (saved where you chose), their own takeoffs, their own collaboration session. That keeps a 12-sheet working set fast on jobsite hardware, and it keeps your takeoff tree focused on the sheets that carry quantities.
If you later need a sheet you didn't pull, open the original set again and extract another selection — or just open the whole thing. Nothing about the original is modified, ever.