Maybe an overkill but we keep at least 3 (and sometimes 4) copies of each return:

1. Preparer Copy: As produced by software with all pages;
2. Preparer Copy (if applicable): Same as #1 but with offline manipulation;
3. Client Copy: Based on #1 (or #2, if manipulated);
4. Filing Copy: Same as #3 but without worksheets.

We use a PDF editor to make changes to the software-produced copy, where necessary.