Hi 
Try
Tools - Options - Paths
to see where LibreOffice is looking for your templates. Hopefully you can edit that to look in the right place. It is better to have your templates inside your /home along with all the rest of your users data and settings. The full address for the 3.5.x branch is something like
/home/username/.config/libreoffice/3/user/template
Note that inside
/home/username/.config
you will see a lot of folders. Each program has a folder in there for it's own settings and configurations. Some are still in /home/username but are moving to the newer place to reduce congestion and confusion.
Note that username should be replaced by your own user-name, the one you login with. Don't change the 3/user part tho!
Regards from
Tom 
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The problem arises from a change in where the templates are
located: LO 3.5 stores them in a different location
(.config/libreoffice/3/user/template) than 3.4
(.libreoffice/3/user/template).
Suggestion: use the organise templates feature again. If you use
"My Templates as the folders for your templates, highlight it. The click
the Command button and select Update. Perhaps this will cause your
templates to appear.
If this does not work, copy your templates contained
in .libreoffice/3/user/template to .config/libreoffice/3/user/template.
Then organise your templates, highlight the My Template folder, click
the Command button, and select Update from the drop down menu. The
templates should appear.
I used this process to add multiple templates to My Templates, and
it saves time compared to importing one template at a time.
--Dan
I tried what Dan suggested but it doesn't work 
I don't even have a "My Templates" folder in the template organiser wizard thing. I know it was there in 3.4 but it's no longer there.
I copied the template files to .config/libreoffice/3/user/template then clicked the Commands button and Update but then got several "templates already exists" messages and one "Update could not be completed" error.
I've removed all folders from the templates path except the default (/usr/lib/ something) and then added.config/libreoffice/3/user/template and set it as the default for adding new templates.
I'm wondering if there is a glitch in the Ubuntu update.
-- God bless you
Keith Bates