When the TU is open, you do not have to worry about the correct paragraph formatting. MetaTexis does this for you.
Please do not do any paragraph formatting when a TU is open. These will be ignored. You should change the formatting of a paragraph only when the TU is closed.
Do not get confused if the automatic paragraph numbering seems to have vanished or seems to appear in the wrong place (e. g. in the case of numbered headings). It is still there and it will reappear in the right place after you close the TU.