That's correct. If you do your ATPL exams, then get only the CPL during the 3 year period, you don't lose the CPL, just the exam credit.
Should you subsequently just want an IR, you can take the 7 IR exams (ok, 6 exams and one total waste of £65) and get one. However, in order to add a multi-crew type rating to your license you'd have to do all the ATPL exams again. If you have a CPL/IR and no ATPL exam credit, you can do the exams and there's no 3yr limit on them as it becomes a 7 year limit (7 years from the date of your last IR renewal, so can be extended indefinitely).