One work around so you don't lose associated dimensions is to open the IFC models in another Archicad file. Hotlink this file into the main Archicad file. Updates from your structural engineer can replace the previous file but FILE NAMES MUST STAY THE SAME.
If you are not going to be dimensioning to the structural elements, you could just be bringing in the structural file.
When overlaying model files, be sure to pre-agree what point is 0,0,0, in each discipline's file or they won't automatically overlay correctly. If this too late to do this, then the module approach would resolve the inconsistency as once adjusted, the placed instance will retain its location when updated.
HTH
Erika
Architect, Consultant
MacBook Pro Retina, 15-inch Yosemite 2.8 GHz Intel Core i7 16 GB 1600 MHz DDR3
Mac OSX 10.11.1
AC5-18
Onuma System
"Implementing Successful Building Information Modeling"