Comment 3 for bug 1195043

yep, it seems to be exactly that:

"the new file is based on a custom template which the user created based on a document with such modifications"

i guess that makes this a duplicate of one of those bugs

heres what seems to be the best reference:

https://bugs.launchpad.net/inkscape/+bug/479638/comments/7

from Bug #479638 - "file gets mangled due to Object->UnGroup Edit"

a little more prodding with my simple test file and, im not sure, but it seems that at least for this particular case, this could be solved by simply /not/ modifying the transform attribute of the clone during the move.

in my case this was originally transform="translate(0,34.54598)" and when simply "moved to layer above" this was changed to transform="translate(0,-558.8162)". manually changing it back (via the xml editor) to transform="translate(0,34.54598)" fixed the problem.. i dont know how such a code change (ie, modifying the section of code that causes the changes in the transform attribute) would affect other expected behavior, but this would seem to be a pretty trivial fix. is there something i'm not realizing here?