it will work
but there will be some mixes
when you remove the deb you will notice that it doesn't work any more
why ? well because the debs uses the same files of the manual install
it will think that those files were created by the deb
so uninstalling the deb will remove the files

TO STAY SAFE :

stay like this until i release the next deb of battery patch
then remove the manual install and the deb
then install the new one