> Which part of fpc.cfg need to be (re)configured?

Well, if you have this directory layout (as I have:):
/usr/local/lib/fpc/2.0.4
/usr/local/lib/fpc/2.2.0
/usr/local/lib/fpc/2.2.1
/usr/local/lib/fpc/2.3.1

check your fpc.cfg to see if it uses $fpcversion macro.
e.g I have
# searchpath for units and other system dependent things
-Fu/usr/local/lib/fpc/$fpcversion/units/$fpctarget
-Fu/usr/local/lib/fpc/$fpcversion/units/$fpctarget/*
-Fu/usr/local/lib/fpc/$fpcversion/units/$fpctarget/rtl

so that a compiler version will pick the correct files.

Another good thing to do is to make some symlinks in /usr/local/bin (or 
whichever directory you have fpc binaries in)

/usr/local/bin/ppcx64 -> /usr/local/lib/fpc/2.2.0/ppcx64
/usr/local/bin/ppcx64-2.0.4 -> /usr/local/lib/fpc/2.0.4/ppcx64
/usr/local/bin/ppcx64-2.2.0 -> /usr/local/lib/fpc/2.2.0/ppcx64
/usr/local/bin/ppcx64-2.2.1 -> /usr/local/lib/fpc/2.2.1/ppcx64
/usr/local/bin/ppcx64-2.3.1 -> /usr/local/lib/fpc/2.3.1/ppcx64

(note that if you are on a i386 machine you'll have to use ppc386 instead of 
ppcx64)

This way, you can select which version of fpc to use with the -V switch:

fpc -V2.3.1 myfile.pas
will call ppcx64-2.3.1

when you compile lazarus, you can do a
make all FPC=ppcx64-2.3.1
(if you put those symlinks in a directory specified in PATH)

bye,
Giulio
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