I guess you have put the time into an integer field, so you can't store the milliseconds as fractions of a second !?

In that case you might store any new data as milliseconds instead of seconds from now on and differentiate the two formats by size (i.e any number greater than the maximal number of seconds you stored before the switch is automatically a millisecond

You should check that the integer type of the database can get big enough to last for a few years (10 years are 307 billion milliseconds). If not you need to add a new field into your database or change the timestamp field to a real number (if that provides enough resolution)