Well that sucked. Found a very annoying bug (or at least a very poor feature if it's intended). Playing as Venice in the Old Gods start I had managed to get almost all of the trade posts around Italy under my control, and was raking in the money. Had all the posts fully upgraded, and was beating the other merchant republics in the area. Genoa was the only one left standing, and it was pretty beaten down because I was stealing its posts after it had broke free from its king.
Then the king of Italy and Lotharingia at the time vassalized Genoa, within a few years Genoa made a faction and revolted with the help of all the other Italians, and like magic suddenly my entire trade empire went *POOF* with no way to defend against it.
Apparently if another merchant republic "controls" the land (as it suddenly does as the new leader of the revolt) your existing trade posts simply go poof.
The king of Lotharingia won shortly and retook control of all the revolting lands, but the tens of thousands of gold worth of trade posts and upgrades still went poof. I still own the cities that I had taken along the coast, but absolutely none of the trade posts (which I had invested all my money into) are left. If it had come down to a war, I had previously beat the entire Lotharingia/Italy kingdom over a single city that they were trying to take back - so I could have easily defended my posts. But they just disappeared.