You can create a label to indicate the start of the appendix and then read the value of the counter("logical-slide")
at the location of the label. If you are already adding labels to your headings, you can use the last heading before the appendix or the first heading in the appendix. If that is not an option, you can use metadata to indicate the start of the appendix as shown in the code below.
#let page-footer = context [
Slide #toolbox.slide-number out of #counter("logical-slide").at(<start-of-appendix>).at(0)
]
#set page(footer: page-footer)
#slide[Something]
#slide[in the main]
#slide[part of the]
#slide[presentation]
#metadata("This is the start of the appendix") <start-of-appendix>
#set page(footer: none)
#slide[Some slides...]
#slide[in the appendix]