Yes the problem is with qtirreco but unfortunately I do not know what the update breaks. If you say you flashed the eMMC too then you should not be having this problem. try

apt-get remove --purge lirc qtirreco
rm -rf /home/user/MyDocs/qtirreco

and reinstall it

but if your problem is like mine it may not fix it. I had a similar problem with gnuplot where there was something still around after a purge which made it impossible to install again but I never found out what it was.

EDIT: Fixed path as pointed out by Kolos