Fyi, the bug report for anyone wanting to follow it:
https://bugs.launchpad.net/inkscape/+bug/1715408This 2nd file looks like a slightly different situation. It might be helpful to include it in the bug report too. Also, if you could include the PDF files too? You could wrap them up in a zip file.
But it's basically the same -- a clone without parent, masked and clipped. It's just there are 2 (the green strip and the photos).
The green strip is created with 2 (page size) rectangles, each with orphaned clones converted to patterns, clipped and/or masked. The weird thing with the green strip is that the patterns and clipping would not really be needed. The green rectangle which is the original object for one of the patterns is essentially the same thing as the end result, after clipping.
I guess some of that could be a result of other file conversions, before you found it. It's really hard to say, but at this point, it seems like a lot of unnecessary work. So rather than think the original creator performed unnecessary work, it's more likely that a file conversion somewhere, changed what kind of objects are involved. So that it only appears there was extra work, when really there wasn't. (I'm thinking maybe the patterns were created somewhere along the way....maybe clones, but I'm just guessing.)
I'm afraid I can't be much help regarding "procedures". Inkscape can use the command line, but I don't know exactly what's possible. Here's the reference:
https://inkscape.org/en/doc/inkscape-man.html And I know I've heard where people use scripts to work on batches of SVG files. But I don't know how to write any kind of scripts myself.
Moini might be able to give you more detailed info about the possibility of using a script.
This is a long shot. There's a graphics viewer/editor called Irfanview, which is known for its ability to handle a wide variety of formats, as well as work on batches of files. It's around 10 years ago I heard that, so that's why I say a long shot. However, it seems to be still available and supported. And it does have SVG support, via plugin iirc. Perhaps it does not suffer the same bug as Inkscape appears to have?