This page http://26.1911encyclopedia.org/W/WI/WIDDRINGTON... has more information on Thomas, including:
"In 1659 and again in 1660 he was a member of the council of state, and on three occasions he was one of the commissioners of the great seal, but he lost some of his offices when Charles II. was restored."
There is more information on the Council of State here: http://www.pepysdiary.com/encyclopedia/295/
Chart showing the number of references in each month of the diary’s entries.