You asked a good question about if removing the lift can wreck your bus in some way.
The answer is, kind of. Dan already gave you great instructions on how to safely remove your lift.
The part I want to address is that school buses have safety wiring integrated into the bus operational wiring.
Many times, especially with doors and things where someone can get hurt, like a wheelchair lift, there are safety checks installed.
At our school district, depending on the brand and age of the bus, a wheelchair lift could simply work even if a door was closed. In newer buses, you may have to have the door open and seatbelt strap engaged. In really new buses you can't have the engine running, have to flip a power switch in the drivers area and maybe more before the lift will work.
Sometimes, removing a safety check (could be a buzzer indicating a door is open, or locked, or no buzzer because the buzzer isn't connected for some reason) and boom....your engine will not only not start...it won't even crank over.
Point being, make sure you know how your bus operates with all the safety integration. This way, you can determine if you may or may not have an problem if you monkey with it.
At the same time, you can use these as a benefit. For example, if my emergency doors slide locks are engaged, a buzzer will sound and the bus won't crank. This is a good anti-theft device in my opinion, so it stays. The slide locks also secure the doors, so when I leave the bus, I'm not worried about people getting in.
Hope this helps.