My department recently upgraded from CS5 to CS6. We are preparing an InDesign print publication for this year and are repurposing last year's Illustrator and InDesign files which we produced with CS5. When we save each Illustrator file, Illustrator displays the warning message "Saving to a legacy format may cause some changes to your text layout and disable some editing features when the document is read back in. Do you want to continue?" So far, we have been choosing "OK" to continue.
My question is: What is the best practice here? Our illustrations are all statistical graphs using the exact same colors, typefaces, line weights, etc. as last year. All of the people working with these files have CS6. If we continue to save to the legacy format are we likely to have problems? From your experience, would it be better to "save as" Version Illustrator CS6 now?