Follow-up Comment #10, bug #17991 (project mypaint):

Opening a different file resets the numbering now, but creating a new file
does not.  If you have a file with 3 unnamed layers and create a new file, the
numbering for the new file starts at 4.  It renumbers properly if you save the
file and then reopen it.

===

Maybe it would be easier to set the layer names as "Untitled Layer #x" on
layer creation instead of leaving them blank.  You could then use a condition
with a regex match on the layer name to determine if it should be in italics
or not.  For example, in Perl you would do something like "if ($layerName =~
/^Untitled layer #[0-9]+$/) { set_italics(); }" 

I think in Python it would be more like this: 
import re
if re.match("^Untitled layer #[0-9]+$",layerName): set_italics()

(I don't use Python often so that may be totally incorrect...)

Doing that, you'd keep the "This layer has not been named" identification
(italics) in MyPaint, but the names would remain consistent when later used in
another app, such as Gimp, or after re-opening the file.

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