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You started a Search across all files in the second file so it will only ends in when it has finished the first file. That is the search state information that was saved when you started the search to "bye". This state is what allows whole groups of Saved Searches to operate one after the other without revisiting earlier already found locations.
In your case, you closed that chapter and moved to the spot where that search's state information indicates it would have been complete once that file was done, which is exactly what it says.
The search has no way to know you started it but decided to not continue it by manually moving to that earlier file by closing the current tab, effectively telling the search to skip all the intervening matches. Normally when manually hopping around you do need to restart a search if nothing in search terms changes (find, replace, target, conditions).
The file you start a search in matters as it determines the ending state (file). You would need to use the Restart Search button to handle a new search starting from this earlier position so a new search state is set because you did not change the search terms at all. When doing a search sequence one by one where you start the search effectively determines the ending point.
So it was not count or Dry-run that is the issue which is why I could not see what you are seeing.
Still not sure what the "save as" is contributing to this.
So if you want to visit every instance of the search in an epub exactly once in a one by one basis, you start a new search anywhere you want and follow the sequence of matches until it tells you it is done.
If you want to manually hop around from file to file reusing previously started searches with no changes then set your search target to the current file, or hit the restart search button each time so that starting point no no longer matters ... just like old Sigil that drove me crazy revisiting matches I had already decided not to change and forcing me to try to remember my starting point. Old Sigil also made running sequences of saved searches in a search group almost worthless. Which is why it was changed awhile back.
I will look into adding a shortcut for restarting a search to the next release to make it easier to do that.
But learning to set a starting search any place you want and following it one by one until it tells you are done is a much more efficient way to perform search and replace helping to prevent omissions and makes SavedSearch groups more useful.
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