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Docking ports won't undock and cause null reference

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I was just recording a normal Gilly SSTO Base, after landing I docked the base outside the cargo bay of the SSTO, but it was misaligned in the roll section, but when I undock, excrementss happens, first stack overflow, crashed my game. After restarting the game, I want to undock again, first null reference exceptation, then Stack overflow, this time it didn't crash.

I start asking discord for help, on guy suggest to remove autostruts, so i did, but the most bizarre stuff is coming.

First, I undock and the two module separates, but when i switch, I could only switch between the ssto and the base. The two base modules separate further, i even turn one of the module, but it is still one craft. I timewarped and what, the hitchiker module's parts starts disorts, it crash into the lab. And worse is that no matter how many time I quickload the same thing happens and the base won't undock, the game just keep saying Null Reference or Stack overflow. I decide to change to other bases/ stations and attempt undocking, but it was normal, i switch to a future save where the base was aligned, but I can't undock that base. 

Both from the quicksave base and the future base starts with the hitchhiker module before the science module docks.

I first suspect the stack separator, terminated the stack separator and the same thing happens to the base. Another thing to suspect is the hitchiker module since it was mostly fixed, I can't turn that module. The last suspect is the cargo bay.

Log: https://drive.google.com/file/d/128lbVBjugsjNHsK-bK2ycEphFuanqUrB/view?usp=sharing

Quicksave ( where all the madness come from an undock button):https://drive.google.com/file/d/1KgcmCKquiwq7Iau6JiOG0067wxofsZnm/view?usp=sharing




Edited by Sirius K
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I didn't have any luck with KML when I had a similar problem with docking ports.  Basically, I had ship A and ship B docked together and couldn't undock them.  I created a temporary save file with new versions ships A and B on the launch pad.  Then I went into the problem save file, deleted the entire code blocks of Ship A and Ship B, then pasted in the A and B code blocks from the temporary save file, changing the ship positions to match their desired locations.  It was a headache for sure, but it fixed my problem.

Most save files are going to have dozens (or more) of vessels and it will be hard to find your ship.  You can make this easier by going into KSP and renaming the problem vessel something unique like "myvessel123456789"

Edited by arthur106
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KML has an auto repair function that works a lot of the time, but sometimes it cannot fix the issue.  However, it is still useful for diagnosing and pinpointing the error even if you have to manually edit the savegame (which you can do quite effectively in KML as well.

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