To ignore hits in reconstruction, use cdfsoft2 version 4.11.0 and run
CT_TrackingModule.  Use a talk-to to provide the hits you wish to ignore.
The following is an example, which ignores all hits in the next-to-last 
superlayer:

mod talk CT_TrackingModule
  DeadChannelMenu
    DeadChannelList      set "tcl"
    DeadChannelSL        set 6
    DeadChannelBeginCell set 0
    DeadChannelEndCell   set 431
    DeadChannelBeginWire set 0
    DeadChannelEndWire   set 11
  exit
exit