First, how did you measure the rods? If you used a calipers, then the measurement is guaranteed to be inaccurate, (there is too much wishful thinking with a caliper). You need to use a real micrometer to get an accurate measurement for this job. Source: This old Toolmaker.
Second, I don't know the manufacturing tolerances for those rods, but I have to think it's more like +/-.01mm and not +/-.05mm. So I would assume you have irreparably damaged those carbon fiber rods by coating them in grease.
Third, yes the carbon fiber rods have absorbed some of the oils in the grease. This is not good. The good news is, if you contact customer service and talk to them, they can sell you a whole new xy carriage even though it's only available from customer service and NOT their parts store. You might even need a whole new extruder and bearings to banish all traces of the grease.