I can see 3 options here

a) setup a second site / clone your site (multisite i guess) where site a is delivery ony and site b is pickup only (with the relevant items available) and links somewhere to switch between the 2 sites depending on if someone wants delivery or pickup
– relatively easy to do but of course you need to maintain 2 sites somewhat

b) write some js that analises whats in the cart when switching from pickup to delivery and vice versa and show alert as required (or even prohibit switching !)
Use the globally available “wppizzaCartJson” object – should be self-explanetory as to what it what
(the existance of this object is deliberately not documented anywhere as it might still change but for now I cannot see any reason why it should , so its reasonably save for the moment to use – at least for the foreseeable future – but at your own risk)
– needs some scripting but should not be too complicated and avoids having to maintain 2 sites. js only.

c) something based on https://docs.wp-pizza.com/developers/?section=change-prices-of-menu-items-depending-on-day-of-week
with some js too perhaps to alert users plus a number of other things (removing iytem form cart or changing pickup to delivery etc etc)
– probably can be made the most elegent, but by no means trivial

… writing out loud so to speak, I’d personally would probably go for b) in your case

hope that helps