Hey Su1,
It might be worthwhile speaking to your accountant, about whether or not you pay part SSP, or what they are supposed to be getting paid, it may help us with getting the right outcome.
I'm going to leave this open to our wider community, but i do have a thought - if you DON'T want this to be done as SSP, or you're not reclaiming anything off HMRC, it could be better to zero their salary - and then use variable input to apply the phased returns hours/pay.
What are they getting paid for this period? Any answer I give is going to be dependent on that information, I reckon.