It is the palette indexes that are causing you problems.
There are the Same Colors in different areas of that Palette.
When you apply that palette or copy and paste, the Green and other colors will pick up the 1st colors on the palette that are the same... and that is Not the correct Color Slot to keep the same index. That file uses the indexes to have the Civ Specific Colors and that is programed to use particular slots for the same colors found in other slots.
Make a duplicate copy of that file... then after you resize what you want, you will have to make sure the correct palette slot for the Colors are what is used.
The same Green color is on Palette slots 231 and 247.
The same Magenta color is on 208 and 255.
Change the Color of the Green that is used on the palette to something not found on the palette. Add 100 Red for example. Also change the Magenta color. Reduce Red 100 for example. Then after making your changes to the circle change the colors back to their original colors. Check the file with the original file and make sure the same palette number is used.
EDIT: because there are other colors also the same on the palette you will need to change #245 light Blue, #228 Red, #247, Green and #255 Magenta to different colors by adding or reducing the Red, Blue Green amounts for them so they differ from all others. Then you can work on the File and when finished, change those colors back to their original colors so they use the same palette slots. This will take care of the problems concerning working on that file.
Hope this makes sense.