Contracts Lumpsum retro pay question

Good Afternoon,

We use contract pay, Our Employees got paid with lumpsum retro for one time payment.

Once this payment is over then this flag is still there and whenever we do employee position changes this same flag is carried forward to the new effective dated row which is causing some issues on our side. Instead of every transaction go back and check the flag and clear them is there any better way to do the same? Your inputs are much appreciated.

Thanks

RK