Flaps decrease the margin to the stall compared to the clean wing at the same AoA, so it’s plausible advice (if a bit paranoid). It's possible that they're thinking about an accelerated stall in a level turn, or of the lower wing stalling during a descending turn and leading to loss of control.
I think you'd need to be on the very limit of aircraft performance to even be close to those scenarios; a 30° turn only increases stalling speed by 7%.
In a transport category aircraft I wouldn't be concerned. There's a reason the slats sequence first during flap/slat extension.