I think this is a fairly unique circumstance that falls in a "grey" area. It looks to me like these were painted by the former owners to "cancel" the chip? If that is so, I see no problem whatsoever with "cleaning" the chip up.
It is not in the same category as filling in a drilled chip and pushing it off as a whole chip. You removed a removable substance from the chip......no foul in my book.

I should say here that I clean 99% of the chips I buy. I like them better that way. JMHO, but, if I was a serious collector of Colony chips, I would have no problem with purchasing your chip. In fact, it looks 100% better to me!

Now, if you turned around and told me "Here is THE one known example of this chip that was NOT painted" I would definitely say you would be in the wrong......