The problem is that the glycans are treated as ligands and won’t be covalently attached to the protein in HADDOCK (we simply don’t have support for this implemented). So if you want to keep your glycans in proper positions, you will have to define a few distance restraints per glycans to the protein.
Your HADDOCK-tools repo on GitHub (https://github.com/haddocking/haddock-tools) does contain a script that allows you to define such restraints. Check the
Also important as explained in the previous answer, a glycan should have only a single residue name and non overlapping atom naming.