Dammit, you're right. There is a completely different section in Cap804 which says that ATPL theory credit lapses if CPL and IR are not granted within 36 months.
Which if taken literally, means if you already have a CPL/IR and you pass your ATPLs they would lapse after 36 months, unless you get your CPL/IR "granted" again. Daft.
The whole thing is very poorly written. If the OP is still reading this - why aren't you in a plane right now?