When we Askenazim read from two Torah scrolls, the one taken out first is returned last and the one taken out second is returned first. 

But we say “maalin bekodesh ve’ain moridin” – we go up in holiness and not down. So why do we degrade the first sefer by returning it second. 

In case you argue that being out is the holiness of the sefer, then the question becomes why do we reduce the time that the second sefer is out by returning it first?

Not deliberately Purim Torah!