After you copy MQX and drag&drop a .wsd file from a new location, you should clean your build projects, before starting build.
I use MQX in different directory almost every day. I have a "copy" of Freescale MQX installation directory, say in "c:/Freescale/MQX402_copy". The MQX directory structure is maintained. For example I drag and drop
c:/Freescale/MQX402_copy/config/m52223evb/cw10/m52223evb.wsd
into a new CodeWarrior workspace (my workspace is in c:/mycwworkspace). I double check that MQX_ROOT_DIR of all build projects is set to "c:/Freescale/MQX402_copy" under Properties->Resource->Linked Resources->Path Variables. Then I select m52259evb | Debug in the combo box on the CW10 toolbar and hit the green start hammer icon (next to the combo box); everything builds ok.