It entirely depends on how well the makefile
is written.
check following:
Does it provide option like make uninstall
if yes then make uninstall.
else open the make file. run make clean
: it cleans only the compiled binaries from default location (this might be all or this might not be all)
and then check the make install
section of the makefile, check where binaries are getting copied, note those locations and delete directly from those paths.
You should be good then.
After uninstalling the program completely you cab re install it. Thats how you can manually update :)