Is it possible to use IF statements to change AI states?
For example: if this squad has over 50% dead units, then sit in base and just wait for more to respawn, and if over 50% unis are alive, then follow the command list to enemy base.

(script continuous rawr
(if (> (ai_living_fraction [ai]) 0.5) (ai_command_list [ai] [ATTACK_command_list]) (ai_command_list [ai] [FLEE_command_list]))
)

Or, you can use (ai_set_current_state [ai] [ai_default_state]) to try to make them do their default flee settings in their tags, but if you want them to hide in their base, then the top with the command list for fleeing is what you want.