Well, it is normal that PHP did not throw any errors, but that does not mean that SQL didn't. In any case, you are calling importSQL only during plugin install, right? When you simply overwrite the files, plugin is not technically re/installed, just updated with php/html/js code. But, errors will be thrown eventually, when you ask for non-existent columns and data.
Again, when you need to properly update your plugin, keeping older versions in mind, you have to check for the currently active version, then perform special upgrade functions per each scenario, and those upgrade functions should only do the necessary modification to the existing table(s). Check upgrade-funcs.php in osclass core, it is the same principle you can use for plugins. In order for this to work, you must store plugin version @ database.