I am also experiencing the problem of Intralink increasing the version of parts in a modified assembly. If one simply adds an assembly datum and saves the assembly, many parts in the workspace will update as if they have been changed.
It is frustrating and time consuming, and am hoping to find some "off-button" to solve the problem.
We have two work arounds.
1-Delete everything out of the workspace prior to check in, except what has really changed. Sometimes we get an error so use the alternative-
2) Export the modified file to another workspace and check it in from there.
