This is similar to what happened with an anon recently. However, that save was rescued and Prof. 9 posted a save at the part after Colonel. I encourage other people to take the save for the sake of bug-hunting. It's almost at the end of the game and I haven't received any bugs at that point.
Here is the save.
Anyways, here is V3.03 of the patch which corrects this issue.
The main patch is still fairly stable and I've been able to work on Hard Mode now. Prof. 9 recommended a neat idea that would increase the difficulty of the game. You may have already heard of it, but he managed to implement a "Folder Capacity" system. Take a look at the screenshot below.
Here is an empty folder with the maximum capacity available.
When you add chips, the number goes up. It's sort of like real hard drive space and each folder can have a maximum of 1600MB.
Once you reach your limit, you can't exit the folder screen. Here, the folder is using 1639MB out of a total 1600MB. It's 39MB over!
You may have noticed that most of the chips have had their MB raised. This should make it more difficult to make an over-powered folder and will force you to reconsider the folder you'll be using.
Your current Folder Capacity can be checked in the status screen. When you have the maximum regular memory of 50MB, your Folder Capacity becomes 1600MB.
I thought it was a brilliant system. It's something I wish the Battle Network games had implemented sooner. For the first few games, the unique number became almost negligible. Now it will play a bigger role. Currently, I've raised the MB of several chips but it seems to be counter-productive as higher MBs prevent the number of those chips in a folder. You would be forced to use many different chips. I am considering lowering the maximum capacity since apparently there are still several decent folders you can make with that sort of limit. Also, your starting folder exceeds the current capacity, so that will have to be changed as well. Anything can still change. The programs seen equipped in the previous screenshot should not be possible in the final version of the Hard Mode patch. Navi Cust Parts will become a luxury and being able to equip more than 3 would be difficult.
I'm sure expert players will have fun. :)