@inaid
Hi, I also studied your case, and thanks to "New Design from File" I could open your a.f3d file and studied that for a while. I noticed that the file had been changed to "Direct Model" mode and not parametric. In that case fixing individual parts on the timeline would not be possible. I also tried the following methods, illustrated by a series of screen shots based on my painful experience. Depending on what your final method of manufacture is. If you are using this file to make a mold to manufacture the metal parts, or by using CNC to mill out the parts, I would try to first form a "Main Component" then move your two parts containing the cover and the body into this Main Component. That is screen shot 1. As you can see now you have two unstitched patch bodies (without the cover). I then exported your f3d to STEP format. When I opened the stp file in Fusion using "New Design from file" you can see the two unstitched patch bodies had become one unclosed surface body in stead of two unstitched patch bodies. In most of the cases, this STP file could be used to make a solid body by your intended method of manufacture. You will have to polish the manufactured parts and might have to smooth out those particular sections of the body more. But I do think you can manufacture that part using this STP file. Of course you can try to use other programs other than Fusion to edit this particular section but to maintain your present geometry I suggest you to use this STP file to manufacture the parts. Screen shots:
1. The original a.f3d. A Main Component was created, and your two sub components moved into this main component
Two unstitched patch surfaces were present.

2: Exported to STP file and opened in Fusion again, the two unstitched bodies changed into one unclosed surface. But still a solid. A surface has no thickness but for the sack of manufacturing it is fine. Could be acceptable

Viewing the STP file using 3rd party CAD viewer, a solid body could be visualized:

Without the cover:

Maybe you should try this method. Lots of time for big complex files using a lot of patch surfaces, if some sections could not stitched it might be hard to edit. Changing into STP format could be a good way to just "Make the part and forget it". Anyway, to make a mold it is a good idea to export to STP format and transmit to other companies for making the parts. They should be able to read the exported STP files.
Hope it helps you a little.
Best of luck!