The OS/2 2.0 Font Palette tool (see below for changes to be introduced with 2.1) by default installs fonts (both PFB and AFM files) into the "\os2\dll" directory. Win-OS/2 by default installs PFB files into "\psfonts" and PFM files into "\psfonts\pfm". These defaults can be changed; since OS/2 and Win-OS/2 use the same PFB files, the user can save disk space by allowing these to be shared (through installing into the same directory, e.g., install OS/2 fonts into the "\psfonts" directory instead of "\os2\dll".) Note that fonts must be intalled and removed through the Font Palette; if you copy, move, or delete a font file without using the Font Palette, the system configuration files are not updated and all hell breaks loose.
Deleting fonts from Win-OS/2 causes the system to update the win.ini file to remove references to the font, but does not delete any files physically. Deleting fonts from the OS/2 Font Palette updates the os2.ini configuration file and physically deletes the AFM and PFB files from the disk. This means that if you are sharing PFB files between OS/2 and Win-OS/2, you can delete a Win-OS/2 font without hurting native OS/2 operations, since the PFB reamins installed where OS/2 thinks it is. But if you delete an OS/2 font using the Font Palette, the PFB file is erased from the disk even though the win.ini file is not updated, so that Win-OS/2 thinks it is still there.