Yes, just change the location rules or make it inactive. The values in the fields will still be there and ACF will still return them with the standard front end function, get_field(), the_field(), have_rows(), etc.
The you can do
if (have_rows('old_repeater_field')) {
// do one thing
} elseif (have_rows('new_flex_field')) {
// do the other thing
}