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To reproduce:
1. Open map editor from main menu
2. run in the console
3. Click "Save and play"
4. Results (current.log) in:

2946.087 Failed to deserialize mod data for "level". Error: Deserialization error, LuaObject targets to wrong object. Save file is probably corrupted.
2946.098 Error AppManagerStates.cpp:1426: Failed to load saved data for following mods:
level

Save file is probably corrupted.

Selecting a tree (or something else i guess) in step 2 and using doesn't result in an error.

Original bug report (from my mod): https://github.com/Choumiko/FARL/issues/99
I save the player in the global table during script.on_init()

Thanks for the report however I can't reproduce the error you're getting. When I test it, no matter what I do it works without error.

Is there some other step I'm missing?

I installed the latest version of FARL off the mod portal and ran your steps without issue every time.

Just to make extra sure, every click to reproduce:
1. Map editor
2. New scenario
3. Play
4. Escape
5. Save and play
6. Give the scenario a name
7. Save
-> Error

Attached current.log and zipped scenario

There is one "magic" thingy in the script.dat, that iirc refernces a FactorioLuaObject

Edit: Same thing on Linux (steam and non steam version), also same error when replacing step 5 with only saving as a scenario, then loading via Play -> Scenarios

Ok, I found the problem.

It's going to take some time to fix. Basically the make-scenario-from-game logic is completely broken and has never worked with script.dat.

Ok, it's now fixed for the next version of 0.17.