Hi Leanda,
I recently upgraded two sites from WordPress 3.4.2 to 4.2.2 and WPEC 3.8.8.5 to 3.9.4.
Please note that my doing WordPress 3.4.2 to 4.2.2 direct is not recommended by WordPress as it’s more than two major version updates but I had lots of testing done and backups available so went for it ‘big bang’ style.
The issues I found during testing in the development site were.
(1) The WPEC backend function ‘flush theme cache’ no longer works
(2) If I use a free shipping discount coupon then input another order it gets re-applied even if I had cleared the coupon from the checkout page. The checkout correctly shows shipping pricing but the transaction results says the free shipping coupon was applied.
(3) On one of the sites (only) if I don’t have at least one coupon active in the WPEC backend setup I lose the product $ subtotal line from the checkout page – very bizarre.
(4) I had to source a new theme as the old one broke from WPEC 3.8.8.6 +
(5) I had to source a new invoicing plugin as the old one broke from WPEC 3.8.8.6 +
Because of (1) my mandatory first upgrade step was to install the new theme, then flush the theme cache – without the flush the product pages were total rubbish.
I then upgraded WordPress next because until that’s done the WPEC plugin update does not appear in the plugins list.
To circumvent (2) and (3) I created a dummy coupon that no-one knows about and deactivated the free shipping coupon we only occasionally use anyway.
My web hosting includes excellent staging site creation so after lots of testing, finding and learning a new theme and an invoicing plugin going live was very easy.
It’d be very risky to just upgrade the live system. You must test the upgrades before going live.
I hope this helps.
Mike.