Yeah Windows is really wonkus about the SD card with multiple partitions on it and it keeps changing how it handles them too. The important thing to note is that you can overwrite the image again with Win32DiskImager but you need to figure out which drive to actually write to.
If you pop the SD card in and it shows up as 3 new drives, only one of them is writable. If you pick the wrong one, you'll get an "Access Denied" error right at the start. In a most unhelpful manner when you get that error, Windows **reorders all the drive letters** meaning if you selected D:\ to write to, it is very likely that D:\ isn't the D:\ you tried to write to the first time. The best thing to do is try one drive letter, if it doesn't work then completely remove the SD card and reinsert it so the drive letters go back to the same that they were the first time you tried, and then pick a different drive letter.
To clarify, if you select D:\, get Access Denied, then try E:\, that's actually probably D:\ again or maybe it is what was F:\. It is a real nightmare when they changed that a couple years ago.
I just know that with my setup, it is almost always the second drive letter that's the writable one. I use the webui System -> Backup / Flash Firmware to update as much as possible because, like Curtis says, its easier than pulling the card out. Just paste the .gz link in the URL box (preconfigured wifi images are not needed when updating).