Why not install it on the slot you don’t use currently? So the currently working slot stays in a working shape?
Data should not be affected as long as you only flash the partitions an initial install or update flashes and you don’t wipe userdata.
If you don’t want to run a risk of messing up the slots, you can append every partition name (apart from userdata, of course, but you don’t flash that anyway) with “_a” or “_b” when flashing them.
E.g. fastboot flash system_a system.img or fastboot flash system_b system.img would force flashing the system image to slot A or B, respectively.