opening another workbook, when one is already running could open in the same or a different instance of excel
it would appear opening excel by shortcut will open in a different instance of excel, whereas double clicking a file will try to open in an existing instance
you can keep your hidden workbook hidden by setting its primary window to visible = false when opening
change app object to suit
xlapp.windows(1).visible = false
whether keeping it hidden will allow the script to keep running or still fail i would be doubtful about, but you should be able to test what stops the script from running when the new workbook opens, are you using any excel events in your script?
there would be some other things you could try, but you will have to test to see if it can work
your script could create 2 instances of excel, in one open your workbook, lave the other for any additional workbooks to open in, you would have to test, to find if other workbooks open in the first created instance or the last, then open your book in the other, of course any other book opened may open in the last used