The lifters may or may not have bleed down from sitting. But... once you turn the motor over by hand a few times, with the rods and valve train installed, the oil in the lifters will be forced out. So yes.. your lifters will then be collapsed and useless for checking. Ideally you want to check your piston to valve clearance using a solid lifter , an adjustable push rod and lite weight checker springs. Then adjust to zero lash before you check clearance. But... It's not very easy to install solid lifters in these bikes. You would need to covert your Hydro's to solids with a machined slug , and either remove the lifters by removing the top end , remove the lifter retaining pins down inside the case , and then pull out the lifters . OR.. removing the internals of the Hydro lifters through the tappet inspection cover and installing a slug.
Short of doing that... you are going to have to calculate what the deck height change is, and what the valve lift change is and use an adjustable checker rod to get to your final rod length and lifter pre-load. You can bottom out the lifter with an adjustable rod and get to zero lash so you can check valve to piston clearance . And then figure out what your final rod length should be for pre-loading the lifter. Generally... you set your lifter pre-load to half the travel of the plunger inside the lifter. On the Bullets, there is .100" of travel inside a dry and fully collapsed lifter. You should also consider that these top end's GROW with heat , and that will reduce your pre-load when the motor is hot. And you should also consider what vale to piston clearance is, that you find in there when considering rod length and lifter pre-load. If you should float a valve... you don't want the valve smacking into the piston because your rod is too long and your pre-load too much.