I hope this make sense.
I have two video tracks which I have synced. I want to do a pic-in-pic using size and position. I’ve done them before, so I know that I can only layer V2 on top of V1 and not vice versa. Unfortunately, I want to do the opposite - layer the current V1 on top of V2.
Is there a way to reverse their designations or some other work around which does not involve re-doing all the syncing work?
Maybe make two .MLT files, hiding V1 in one and hiding V2 in the other, then in a third project file, “Open MLT As Clip” for V2 and V1. I haven’t tested it, and you might need to add some kind of background/chromakey thing too, but I think it would work…
Here’s a thread that might help you move the video tracks.
The video posted by @qubodup in post #6 works.
Nice reference @sauron. I was thinking about that same workaround that @qubodup made a video about, but I didn’t really want to guide someone into editing mlt files, as I wasn’t sure how to edit the change myself. Now I know what to look for. 
I tried the two suggestions. Neither one worked. Even renaming the clips per @sauron’s link didn’t change which clip could be overalyed using the Size & Position filter, so there is probably something else in the XML file controlling that property.
The solution I am working on now is to export the tracks separately, and then start a new project. It appears they export in their “synced” positions. IOW, V2 in the timeline starts 2 minutes into the project, the resulting mp4 will be blank for the 1st 2 minutes also.
As I recall it, Dan made changes to V1 (June versions) in that the composite state is always disabled. (Re)Naming is probably arbitrary and makes no difference to this state.
I think that’s what I found.
My solution of exporting what I had to mp4 and then creating a new project seems to have worked. I guess I just have to think about which is the “main” video and which is the “layered” one in advance.
V1 should always be the main/background video. Think of V1 as the bottom layer.
I just tested this on a sample project (didnt test any further after seeing the tracks though). First make a copy of your project MLT file and then work on that file only.
Open the MLT file in a Text editor.
playlist0 variable corresponds to track1
playlist1 variable corresponds to track2
Follow following steps
(this is assuming there are no filenames contains strings like playlist0 or playlist1)
Similarly you can also exchange references to “V1” and “V2” strings.
Now open this modified MLT file in SC. Above procedure would have exchanged compositing effects of V1 and V2.
I havent figured out how to change the up-down position of tracks though.