Thanks for the report. I'm not quite sure what to make of the information, so i'm wondering if you can provide a file, along with step for step instructions what i should do to replicate the issue.
Also, just to rule out a common source of confusion: Moving/Swapping content from an even to odd, or odd to even position will always 'mess up' attributes. That's an inherent property to the low resolution of the NES's internal attribute memory, which is one palette ID per 2x2 tiles, ordered in even intervals. In case the swap creates more data than the attribute resolution can hold, overwrite will occur.