The notes to be
unchanged should not be selected (the "Search" dialog of the pair), otherwise they will be changed. So run Search/Replace once for durations 0-100, setting the "Replace" length to 100-100, then again for 5:200 - maximum, setting the "Replace" length to 5:200-5:200.
Looks like what is happening is the selected length range 0-2236962:1xx is being arithmetically collapsed to 100-5:200. All your notes are extremely short compared with 2236962:1. so they are all mapped to 100. For example, in order for one of your notes to be mapped to 5:200 with your Search-Replace parameters, it would have to be 2236962 beats long. In order to be mapped to 101, a note would have to be 456:502 long.