I always type up an explanation of the issue and fold it into my logbook (so they can see it if they review it without you present and able to explain). Clearly state something like "logbook PIC column includes dual rec'd time logged as PIC in accordance with CFR 61.xx (the sole manipulator rule) - please note that this has been reworked on my application to indicate PIC only as the time solely responsible for the aircraft".

Seems to work for me.