I put up a fixed version 1.1 of the Change Color Plugin at sourceforge:

https://sourceforge.net/p/sweethome3d/plug-ins/14/#9ea3

The plugin now preserves the existing alpha (transparency) of an item's colour. This means that visible things should stay visible.

I also added a special case to restore the alpha of item's broken by the bug. If a colour is changed to itself, the alpha is set to the alpha of the new colour (which is always FF). So I made all my kitchen cabinets visible again by changing colour #E5E4DB to the same colour #E5E4DB. (Manually un-setting invisible causes the colour to be lost).

Lastly, I fixed a bug where the plugin was failing to detect when a texture was present (if a texture is present it overrides colour).