Everything that is based on old-style WB v40 planar icons is only capable to write back the planar images onto disk without a palette when you save any changes that you have made to an icon. WB v40 and all related tools don't know anything about the color mapped images of the OS 3.5 format. With a fixed palette you may not see the damage, but the extendxed OS 3.5 icon information will be cut off by most WB v40 icon tools.
SwazInfo is already clever enough to avoid writing back the complete old-style icon DiskObject-structure onto the disk when it detects a palette mapped icon. It will just change the tooltypes. the default tool, the stack size and the icon type, but it won't destroy the image.
It's correct that using the workbench.library v44+ will also fix this problem. With a workbench.library v44+ you can even drag and drop icons into the WBInfo window.