From my recent experience, the rule of thumb is:

(1) If you switch to an AC operated flight, you will be put in R class and seated in J;
(2) If you switch to a partner flight in an AC flight number (codeshare), you will be put into your original class and seated in Y/PY; and
(3) If you switch to a partner flight in its own flight number, you will be seated in J and put into a fare class corresponding to a J cabin (can be J, D, P, C, or Z, I saw them all).

The change will not affect the confirmed upgrade in your other bounds.

However, I have also seen for award flights in AC metals, it can be put back to fare class I/X and you lose your upgrade.

In the end, just as other suggested, always check the "Details" before making the change.