I've recorded a Screenr that demonstrates changing all instances of the <NotesHeightSmall>550</NotesHeightSmall> in one click of a button. It does require you to download and install the free utility Notepad++.
1. After publishing your presentation, navigate to the data folder of the published output.
2. Open the presentation.xml file in Notepad++
3. From the Notpadd++ search menu, select Find...
4. From the Find dialog, select the Replace Tab and enter the following text as shown below.
*Note: Make sure the Regular Expression radio button is selected under the Search Mode group.
5. From the Find dialog, select the Replace All button.
6. Save and close the modified presentation.xml file.
You might find with large presentations and until this issue is addressed, this can save you a lot of time.
I hope this speeds things up for you!