Hope you are doing well and sorry for the trouble. As described the highlights are getting disappeared from the PDF file.
Would you mind sharing the version of the Adobe Acrobat/Reader DC and the OS you are using? To check the version of the application please go to Help > About Acrobat and make sure you have the latest version 20.13.20074 installed. go to Help > Check for Updates and reboot the computer once.
Also, make sure that the Filter setting is set to show all comments. Open the file and then open the Comments panel and click on filter icon > Show all comments.
In general, you should be able to save you annotations when a document does allow these types of modifications. Are these documents protected? Please check the document properties and see if changing the document and commenting is allowed or not.
Open the PDF > Go to File > Properties > Under the 'Security tab' check for any restrictions.
Also please check if you are able to see the highlights in other documents that you've saved and re-opened.