I've been told that there are some weird cases when routing is changed. For example HEL-AMS Y flex is booked to S-class for 300 euros. Then you try to change that to HEL-FRA N-class ticket which is priced for example 200 eur. AY won't return the 100 eur because they somehow use HEL-AMS N-class pricing which could be like 500 euros resulting to 200 fare difference to be paid.

Problems also arise when booking flex tickets during promotions. Tickets can end up to the W-class which won't be available after the promotion. It is always wise to change these tickets only after the first segment is flown.