I have the calipers and master cylinder off, is it ok to spray brake cleaner in the metal lines and blow them out with compressed air? The rubber lines are being replaced with new, so I'm talking about only the metal lines here.

no problems.. but why? has the system been open?

Related question- my system is open while I fix rust issues... Any tips on how to treat the lines and cylinders while they're sitting around waiting to be reinstalled?

if they are open for a short time then really nothing needs to be done (couple of months) other then capping the ends.

However if they are open for longer they should be blown out to remove any fluid in them as we all know brake fluid loves to soak up moisture and this can lead to corrosion on the inside.

my 2 cents...

Years ago I sanded the rust off of my brake lines on my 68 VW, treated with POR metal ready (outside only) and then sprayed with clear rustoleum. Stupidly drove the car through many north east winters and they never rusted. Rest of the chassis was turning to dust of course.

Brett