I can see your point now.
Materials are Project Specific. If you are Linking into your LT Project a Project that was created in full Revit - with Materials that have Thermal and Physical Assets - the Link is not getting those Materials from your Project. The Link is using its own Project Materials - even if the Link's Material Name is identical to a Material Name in your Project. So, you can delete Materials from your Project without affecting the Link Materials.
However, if you load into your LT Project a Family (RFA) that was created in Full Revit - with Materials that have Thermal and Physical Properties - and you assign a Material from your LT Project to that Family and then Open, Edit and Save the Family, those original Thermal and Physical Properties will not be preserved. Also; and I'm not to sure about this one: since Project Materials RULE over Family Materials, the Thermal and Physical Properties in the Family Material may not be preserved upstream. What I mean by "Rule" is that if the Project and Family both have an identically named Materials, the one defined in the Project is the one the Family uses.
We need someone with both LT and Full Revit to verify this. Unfortunately, I've never used LT.