Using PKGBUILD to build after hacking/changing sources?

I'm trying to hack a MSYS package, so I found https://www.msys2.org/wiki/Creating-Packages/ - as an example:

git clone "https://github.com/msys2/MSYS2-packages "
cd MSYS2-packages/flex
makepkg -sCLf

So, if I run this, I get the sources built, and I get a package. Now, let's say, I change something in the source of the flex package, and I want to rebuild. I tried the makepkg -sCLf, but that command actually deletes the source directory - including my hacks - and so, that command in particular, cannot be used to build a package with hacks/changed source files. What command could I use instead, to build (hopefully only) the changed files in the source, and to build a package from that source?