Hi Hilaire.
Probably there is some case where Calypso do not react on particular system changes. Internally it maintains the cache which needs to be invalidated.
I did a lot of recategorization during my work and I did't saw such problems quite a long time after I fixed last related issue. If you will give me reproducible case I will be able to fix it,
If you will encounter it again you can clean the cache manually using:
ClyNavigationEnvironment reset.
It requires reopening browser.
One question: did you perform all modifications from Calypso?
Best regards,
Denis