I had the same issue on a ST RTW - I had to break my RTW to return home for some family business, and joined my RTW in mid-journey. The route was supposed to be:

PEK-NRT-KIX
KIX-AMS-BCN
BCN-FCO-TLV

but since I had to go home, it became:

PEK-AMS-TLV - this was originally a R/T, but I made a "stopover" in AMS to rejoin my RTW...
TLV-AMS-BCN
BCN-FCO-TLV

I lost the AMS-PEK part of the R/T

I tried being "honest" about it, but KLM actually told me to cancel the KIX-AMS portion and to rip up the coupons PEK-NRT, NRT-KIX, KIX-AMS.