Complex sentence: If they had not been lost by this time they certainly went astray during the French Revolution when the Scots College was itself under threat and its records and valuables were moved for safe-keeping out of the city of Paris.
Split into simpler sentences: If they had not been lost by this time, they certainly went astray during the French Revolution when the Scots College was under threat. Its records and valuables were moved for safe-keeping out of the city of Paris.