I got really far in 0.59, and I saved it at the bottom of the save list. But when I opened 0.61, I couldn't find my save. Is there any way to fix this? I don't want to have to start all over every time there is an update.

RPGMaker games like this save their files within the game folder directly. So, if you wanna transfer your save files, go into the game folder of the older version, then the www-folder, and copypaste the save-folder into the new game folder (all of it, including the config and the global file). Be warned though, this can potentially cause problems. The RPGMaker tends to highly dislike loading older save files into versions with new scripts. That's why each update comes with a save-folder with prepackaged save files, so people won't have to start from scratch every single time, and can just jump straight to the parts that are new. I don't know where you last saved, but the savest bet would be to use a save file from before you first entered Piratetown. Like I said, this doesn't have to cause problems, but it did for some people in the past, so if you use an older save file, and you end up stuck in an area, cutscenes not playing, important NPCs or items not showing up etc, this is why.