Just for note to others who are new to FPC/Lazarus and might get, just like me, confused with used terminology.
I needed to rebuild RTL and various FPC libraries that rely on it. Not the FPC as whole, but its libraries (packages).
Since I had standard Lazarus installation, I didn't have sources for packages, so I went to github mirror and downloaded FPC trunk.
Directory structure on my machine is:
c:\lazarus\fpc\3.0.0\sources\
sources\rtl had rtl sources, but there was no sources for other modules (fcl-base etc), so I copied over rtl\ and packages\ to my source folder from trunk.
Then using "make clean", "make all" and "make install INSTALL_PREFIX=c:\lazarus\fpc\tmp" I was able to rebuild needed modules. First doing it in \sources\rtl folder, then in sources\packages.
After that I needed to copy over c:\lazarus\fpc\tmp\units to my c:\lazarus\fpc\3.0.0\units to finish the process.
Topic can be closed.
Thanks everyone for replies, really enjoying community.