Known Problems with the Transfer Project Standard Tool
Here are some known problems with this tool which Autodesk has acknowledged are on their list of issues.
Filters and View Templates
If you transfer Filters and View Templates together to a project where View Templates and FIlters with the same names already exist there are two types of problem, one simply annoying and the other project-breaking.
If the filters already exist they will often be renamed. But handled correctly this is a trivial issue.
There is no known workaround.
If the View Templates already exist their new realtionships to Filters will not be transfered.
Existing View Templates in the destination project of the same name as View Templates from the source project need to be deleted before attempting to use Transfer Project Standards.