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?
Best answer I can give without seeing the actual files is....... Possibly.
If you work in CS6, then save to CS5 or any previous version (legacy) you can find the files have changed. Appearances can be flattened or expanded when saving to legacy formats.
For example, the Gaussian Blur was updated in Illustrator CS6 (and vastly improved). Gaussian Blur is used for all drop shadows, feathering, glows, and obviously blurs. This means if you create anything using the Gaussian Blur in Illustrator CS6, upon saving to a legacy format, you'll find the blur object has been expanded and is no longer "live" and editable. This can create additional work if the file needs to be edited again in the future.
Gaussian Blur is simply one example. Essentially, anything which utilizes newer features is subject to alteration. Gradients on strokes, transparent gradient stops/meshes, etc. They can all cause issues.
If everyone has CS6 and is working in CS6, I'd suggest, upon editing, saving to CS6 format.
The obvious exception would be files which are flat files in nature, containing only basic fills, strokes, or text without any advanced appearance settings.
My general practice is use the legacy files all you want with Indesign. But if you must edit a legacy file, re-save it to the native format for whatever version is being used to edit the file.