A quick test shows that if a cell has conditional formatting such that
it has a background color set by the conditional format, changing the
column color doesn't change the conditional formatted backgrould color.
If you have just one color you want to remain unchanged, you could
write a UDF (user defined function) that would return a True if the cell
had the background color. Then maybe you could use that function in the
rule portion of a conditional format that would set the background color
of the cell to that color.
It sounds odd - a conditional format to set a cell's background color
to color X if the cell already has color X as the background color, but
it might work to keep setting an entire column's color from changing
cells with the specified color.
Another possibly useful tidbit is that if a cell is merged with another
cell, changing the column color of any or all of the columns the merged
cells were in won't change the color of the merged cells - but trying to
use that may have a lot of other side-effects in your workbook.