It seems that this behavior reproduces on my side with svn, version 1.14.2 (r1899510) on Windows. I'm not sure if my reproduction script is correct, but the behavior looks similar.
The file unversionedfile.txt is missing after the svn client automatically solves the tree conflict when updating a working copy.
Here is the script (Windows Batch):
[[[
mkdir C:\marcel-bug-report
svnadmin create C:\marcel-bug-report\MyRepo
svn mkdir file:///C:/marcel-bug-report/MyRepo/MyDir -m "Adding a new directory"
svn checkout file:///C:/marcel-bug-report/MyRepo/ C:\marcel-bug-report\working-copy-one
echo foo > C:\marcel-bug-report\working-copy-one\MyDir\myfile.txt
svn add C:\marcel-bug-report\working-copy-one\MyDir\myfile.txt
svn commit C:\marcel-bug-report\working-copy-one\ -m "Adding a new file"
echo bar > C:\marcel-bug-report\working-copy-one\MyDir\myfile.txt
echo baz > C:\marcel-bug-report\working-copy-one\MyDir\unversionedfile.txt
svn move file:///C:/marcel-bug-report/MyRepo/MyDir file:///C:/marcel-bug-report/MyRepo/RenamedDir -m "Renaming a directory"
svn update C:\marcel-bug-report\working-copy-one
]]]
[[[
C:\Users\Lyalyakin>svn update C:\marcel-bug-report\working-copy-one
Updating 'C:\marcel-bug-report\working-copy-one':
C C:\marcel-bug-report\working-copy-one\MyDir
A C:\marcel-bug-report\working-copy-one\RenamedDir
A C:\marcel-bug-report\working-copy-one\RenamedDir\myfile.txt
Updated to revision 3.
Summary of conflicts:
Tree conflicts: 1
Searching tree conflict details for 'C:\marcel-bug-report\working-copy-one\MyDir' in repository:
Checking r3... done
Tree conflict on 'C:\marcel-bug-report\working-copy-one\MyDir':
Directory updated from r1 to r3 was moved to '^/RenamedDir' by Lyalyakin in r3.
A directory containing uncommitted changes was found in the working copy.
Applying recommended resolution 'Move and merge':
C C:\marcel-bug-report\working-copy-one\RenamedDir\myfile.txt
At revision 3.
Tree conflict at 'C:\marcel-bug-report\working-copy-one\MyDir' marked as resolved.
Summary of conflicts:
Tree conflicts: 1 remaining (and 1 already resolved)
]]]
[[[
C:\Users\Lyalyakin>svn status -v C:\marcel-bug-report\working-copy-one
3 3 Lyalyakin C:\marcel-bug-report\working-copy-one
3 3 Lyalyakin C:\marcel-bug-report\working-copy-one\RenamedDir
C 3 2 Lyalyakin C:\marcel-bug-report\working-copy-one\RenamedDir\myfile.txt
> local file unversioned, incoming file add upon update
Summary of conflicts:
Tree conflicts: 1
]]]
--
With best regards,
Pavel Lyalyakin
VisualSVN Team