Hello Awt104,
Apple Support Communities is a wonderful place for help with the Notes app on your iPad, and we know how important it is for Markup edits to save. To confirm, are you tapping Done before switching to another app to confirm those changes are being saved? If not, make sure to tap Done before switching applications. This information can also be found in the article below.
Mark up attachments in your notes on Mac
If you continue to have issues after tapping Done before switching apps, you may find the following article helpful. While the title of the article outlines different issues, these steps can help resolve many application specific issues.
If an app on your iPhone or iPad stops responding, closes unexpectedly, or won't open
Let us know how that goes!