It happened because GiveStatusEffect removed superweapons status effect and this code block added it back.
if(!StatusEffects_active(STATUSEFFECT_Superweapons, e))
{
- if(!g_weaponarena && (STAT(WEAPONS, e) & WEPSET_SUPERWEAPONS))
+ // also give default superweapon time if player had no superweapons and just got one
+ if(!g_weaponarena && !(save_weapons & WEPSET_SUPERWEAPONS) && (STAT(WEAPONS, e) & WEPSET_SUPERWEAPONS))
StatusEffects_apply(STATUSEFFECT_Superweapons, e, time + autocvar_g_balance_superweapons_time, 0);
}