Since IconDeveloper and Iconpackager's recent difficulties working together. ( trying to recolor a package with ID makes the Iconlibrary unreadable by Iconpackager).
I have devised a way to still be able to recolor Icon packages,with as little difficulty as possible. As well as not having to totally rebuild the icon packages from scratch.
To recolor Icon packages without rebuilding the package. First open iconpackager and select settings, In the "saving icon packages" section make sure to tick the "save package as individual icons" box and apply. (This will give you Icons to recolor out side of an ICL and tell IP to use these individual icons instead of using the ICL).
Then select the IP you want to recolor and apply it. After it has applied press ctrl-s or go to the tool bar at top and under "file" use the "save: option. (This will actually have IconPackager extract the icons from the Icon library and place all individual icons within the icon packs folder.)
There are many ways to recolor them, I will detail the 2 easiest.
#1: SkinStudio5 batch processing.
Now,If you have SKS5 you can open them all up with batch processing. Open Sks, then click "file", in the menu select "Batch processing", in the sub menu select "Recolor images in a folder" and click. Within the selection window that opens two selections will apperar. In "source folder"Browse to the folder where the icons are you wish to recolor and press ok. Do the exact same for "target folder",
Target and source folders must be the exact same location for this to work properly, (saving to another folder will save the recolored icons to somewhere else and the iconpackage will not see them.) After you have done this click "next". Now SKS will open the icons in the recoloring window. Recolor your icons as you wish and press "OK" this will save the recolored icons.
Now you can open Icon packager and apply the freshly recolored package

#2: Icon Developer.
Open Icon developer and select recolor icons . then find the icons you wanted recolored and select them all. In the next window that opens select the same folder your icons are in, this way they will be seen by the Iconpackager later and press OK. Now the icons will open in the ID recoloring window (they will be recolored one at a time but they are all loaded), recolor the first icon and press "apply" then press next. You will now see the next icon appear to be recolored, repeat this process until you have reached the last icon to be recolored and the finish button appears, recolor the last icon and press finish.
Now you can open Iconpackager and apply your freshly recolored icons

Hope this helps.
HG

Versions #s of the programs used are as follows.
IconPackager: 3.20(a) rc(.033)
SkinStudio5: 5.0.1 Build 1112
IconDeveloper: 1.9.7.0