System Information
Operating system: Linux-5.4.0-7634-generic-x86_64-with-debian-bullseye-sid 64 Bits
Graphics card: GeForce GTX 780 Ti/PCIe/SSE2 NVIDIA Corporation 4.5.0 NVIDIA 440.100

Blender Version
Broken: version: 2.83.4, branch: master, commit date: 2020-08-05 06:00, hash: rBc113af82881a
Broken: version: 2.90.0 Beta, branch: master, commit date: 2020-08-07 15:11, hash: rBa93be410c974
Worked: version: 2.82 (sub 7), branch: master, commit date: 2020-03-12 05:06, hash: rB375c7dc4caf4
Caused by rBf7386b97571e: Fix T62612: Saving with "Remap Relative" makes ALL paths relative

Short description of error

• I hope I can make this clear.
• I'm using Linux (Pop!_OS 20.04)
• I'm using Factory Defaults.
• I included the whole project (simplified) as .zip to this report.

• So, I'm working on a project and want to organise the folders a bit better. I want the Video Editor file comp_0001.blend to be located from /3d/comp/comp_0001.blend to /comp/comp_0001.blend.

Here is a capture of how files were and how I want them to be - As you can see, the COMP folder should locate at the root of the project:

• So, I just though of using 'Save As...' and keep the Remap Relative option ON, as usual.
• But then all the frame sequences get this on their source frames:

Very weird. The folder 3d gets duplicated a lot of times. And of course the frames don't work anymore, since the path is incorrect. I think this is a clear bug. And I think a lot of people want to reorganise their folders like I do.

Exact steps for others to reproduce the error

• Unzip the file structure
• Make Blender to use factory defaults
• Open /main_directory/3d/comp/comp_0001.blend
• Notice how the .png frames get loaded normally (hopefully, should load nicely, they use relative mapping for path)
• Save the .blend as /main_directory/comp/comp_0001.blend
• notice how the .png frames' source gets messed up :(

Attached file structure with the .blends and source frames to make it easy to reproduce (hopefully):