Previous to the latest patch, I had collected all weapons, tiles, masks, and unlocked every map. The game was still very crashy, though, and I had heard windowed mode support was being added in. Thus, I installed the patch. It seemed like it was a full game reinstallation instead of a patch, though.

Now the game does NOT recognize any progress. All maps locked, no masks, no tiles. Everything back to square one.

Is there a way to fix this? It's very frustrating.

Support for windowed mode is supposedly coming in the next patch which may come over the weekend which means it should get in here by Wednesday.

Now, the saves are in your previous game folder if you're on Windows XP. The new installer puts the game into a different place so that's why it seems your saves are gone.
In Windows 7 your saves should be in a hiddden folder C:\Users\yourusername\AppData\Local\VirtualStore\Program Files (x86)\GOG.com\Hotline Miami

A couple of other people had the same problem as you and discussed it here:
http://www.gog.com/en/forum/hotline_miami/new_version_of_hotline_miami_is_ready_for_download/page1

In short, locate your save files (saves.dat masks.nfo achievements.dat) and copy them to your current game folder (most probably C:/Hotline Miami)

If you're using XP like I am, check to see it didn't install in a different folder. My previous install was in "GoG.com" folder. The new install wanted to go in something like "GOG Games" folder until I overrode it. If it's in the new folder just copy the old save files over to your new installation.

edit: oh previous poster pretty much said what I did.