Element IDs are assigned installation specific, meaning that the IDs are assigned when the element is first installed and that the IDs for an element can differ between installations. Applying a hotfix or a Cumulative Update (CU) separately in 2 different environments might cause element Id differences and hence Id conflicts.
The recommendations on how to avoid this are given in the following TechNet article which outlines installation specific IDs and element handles (http://technet.microsoft.com/en-us/library/hh352326.aspx).
It is also recommended to follow the same deployment guidance for hotfixes and cumulative updates that is used for customizations in order to preserve IDs across environments. Please download and read the Whitepaper, Deploying Customizations Across Microsoft Dynamics AX 2012 Environments from http://technet.microsoft.com/en-us/library/hh292604.aspx.
In Summary, this means that, if you have two AX 2012 environments (Source and Target), you have first to install the Hotfix or CU on one of those (Source), run the Full compilation, Synchronization, Full CIL generation, etc.. and move the entire ModelStore to the other environment (Target).