Why do airports remove/realign runways?
In some cases the prevailing winds change and certain runways fall out of use. Since airports tend to be land limited they may wish to use the land for hangars or other facilities so the runways are eventually decommissioned.
In other cases it could a noise abatement issue, many airports predate the property development that often surrounds them. It may be in the best interest of the local neighborhood to change the runway orientation to one that creates less noise and pollution over homes or businesses.
In some cases runways may be moved to comply with changing regulations as was the case at Aniak Airport, where an existing runway no longer complied with obstacle clearance regulations.
In some cases it also becomes expensive to maintain a runway that may not see much use and it will be shut down.

Magnetic shift generally wont cause a runway move but it may cause a runway re-number since the runways are numbered as per their magnetic heading.