I agree with the others that, so long as it is clear, there is no issue whatsoever.
I have a similar story to Partninja's, albeit for different reasons, thus I agree with him very strongly here. I started out as an Alaitoc player, following the colour schemes in White Dwarf for the GW studio Eldar army of the early 1990s. Over time, I shifted away from Alaitoc to my own craftworld, which has a totally different colour scheme, so I just wrote a narrative to explain it. In this case, they were a splinter faction which broke away from Alaitoc, thus they still have some troops and vehicles which are still in Alaitoc colours.