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    $\begingroup$ After you paste back into a notebook, you can select the cell and press Ctrl-Shift-N to format it as StandardForm. This will change the Subscript to look like a subscript. It will also do some other formatting, some of which may not be desirable (e.g. remove all newlines). $\endgroup$ Commented Feb 28, 2014 at 15:07
  • $\begingroup$ @Szabolcs: Thanks, that seems to be a usable workaround, if you post as an answer I'll mark it as resolved. $\endgroup$ Commented Feb 28, 2014 at 15:13
  • $\begingroup$ Well, I didn't post as an answer because there's enough undesirable formatting done by it that I didn't find it very usable myself ... $\endgroup$ Commented Feb 28, 2014 at 15:17
  • $\begingroup$ @Szabolcs: When you say "undesirable", do you mean that it can potentially execute incorrectly after pasting and Ctrl-Shift-N, or that it aesthetically looks bad? $\endgroup$ Commented Feb 28, 2014 at 15:18
  • $\begingroup$ It just looks bad, as in less readable. My biggest problem is the removal of line breaks. It should never execute incorrectly. $\endgroup$ Commented Feb 28, 2014 at 15:19