Sync VST instruments?

A while ago I made a little ambient loop with a melody. For listening purposes I wanted to render the same two patterns in sequence 4 times with some silence before and after. However, adding silence at the beginning in the form of a pattern with only 1 or 2 lines results in the internal LFO of one of the VST instruments I use to be desynced from the actual start of the song, resulting in dramatic changes to the overall sound. It’s a bit of a problem when starting realtime playback in the middle of the song as well. What is the best practice to deal with this?