OK, found a way around this - use home menu/sort and filter button and choose filter. From the top line, choose Filter by Color and select the required colour. Then mark up the filtered records by putting in some text (I use 'x') and dragging down so it populates all the lines in the filter. Then toggle the filter off again. The data can now be imported into a program that does not support cell colours and you have the 'x' to show which records were marked up.

This is a decent workaround for me, but I'm still curious as to why find/replace by format no longer seems to work. Does anyone have an answer for this?

Cheers