System Families which has a relationship to other system families must be transfered at the same time for their relationship to be maintained. For example, Text Types, Arrowheads and Dimension Styles need to be transfered at the same time so the system families they refer to in their settings (both Text Types and Dimension Styles make use of Arrowheads) are in place and maintained.
Another typical example is that View Templates and Filters must be transfered in the same action to maintain their relationships.
Elevation Types do not transfer with TPS. Types for Elevation Tag and Callout Tag are transferred including the Families they use.
Settings for Revit Links are not maintained when transfered, even if the destination project uses the same linked projects.
Section Types (including Detail View Types) do not transfer with TPS. Types for Callout Tags and Section Tags are transferred including the Families they use.
If the View Templates you transfer already exist in the destination project not all settings will be transfered. Small changes are disgarded and Filters, even if set to transfered at the same time, are not transfered. For details see the discussion forum entry ' Trouble transfering View Templates and Filters between projects'
There are also limitations with View Template settings for Revit Links.