Just a guess, but you may have to delete the old biblepay dir:
rm ~/biblepay -r

Then to upgrade the sanc:
cd ~/biblepay-evolution (or wherever this is) sometimes its cd /biblepay-evolution (etc).
git pull origin master
make
(This assumes you built it from source before).

We are up to v.1.4.3.9:
https://github.com/biblepay/biblepay-evolution/commit/693d141d983af2d1982847d51eaa85946ce7e858