Please follow the steps to remove boxtrapper completely :-

rm -rf /usr/local/cpanel/base/frontend/x/mail/boxtrapper.css
rm -rf /usr/local/cpanel/base/frontend/x/mail/boxtrapper.html
rm -rf /usr/local/cpanel/base/frontend/xmail/mail/boxtrapper.html
rm -rf /usr/local/cpanel/base/frontend/xmail/mail/boxtrapper.css
rm -rf /usr/local/cpanel/base/frontend/x/pro/boxtrapper*
rm -rf /usr/local/cpanel/base/webmailboxtrapper.cgi
rm -rf /usr/local/cpanel/etc/exim/per
rm -rf /usr/local/cpanel/etc/exim/perl/boxtrapper
rm -rf /usr/local/cpanel/etc/boxtrapperrm -rf /usr/local/cpanel/bin/boxtrapper

Go to WHM uncheck the option for boxtrapper in Tweak Settings the go to Feature Manager->Edit default feature option and uncheck it from there as well.

cp /etc/exim.conf /etc/exim_bak.conf

And remove all the instances of it from /etc/exim.conf

Save and restart exim.