How about incrementing the version number by an amount proportional to the lines that have changed in the code base. So 10% of lines have changed and 20% of lines have been added, so increment version number from 5.6 to 7.28.
Lines of code are even less meaningful than version numbers.
There are some good standards out there for versioning. But honestly the best thing you can do as a developer or sysadmin is to treat every version update like a breaking change and run it through your dev and test environments before pushing to prod.
With my tongue firmly still in my cheek, I'd say increment the version number by the difference. So if you deduct 5% of the code and add another 15%, then increment the version number by 20%.
