Possibly you need an updated BOOTOS2, which is the micro filesystem that is just smart enough to load os2ldr, which is smart enough to find \os2 and \os2\boot
Generally the Arca Noae packages run fine on Warp v4 and are licensed to do so. My Warp v4 partition is still HPFS so I never noticed any problems with booting with the updated JFS. Biggest problem with my 20 year old install is it traps within a minute or so of the WPS coming up if I use more then one core. Snap doesn't like my monitor either.