Thanks for the replies.
I had documented the experience here on the wiki:
http://www.os2world.com/wiki/index.php/Experiment:_Moving_the_OS/2_Directory_StructureI had failed with this two directories:
1) MMOS2 a) CWMM seems to give some problems moving it,.
b) System sounds keeps poiting to the sound scheme to the wrong locations.
c) UniAud driver sound loop bugfix got broken.
2) LANGUAGEa) UNICODE.SYS on boot does not recognize the new location of the files.
Also testing:
DESKTOPThe desktop seems very safe to be dragged and drag and drop on other location. On my case I move it to \Home\Default\Desktop
Everything seems to work fine with it.
Maintenance DesktopI haven't tried it yet. What do you think? do you know which INIs has its location?
I will try it later with "Maintenance Mode" and see what happens.
I want to try later movig etc, usr and var, since they are necessary of the all the RPM/YUM stuff, but I was told It was not much of a trouble moving them.