Red line records

I suggest retiring the Multi Choice Text field and replace it with a relationship.   For example:

Perhaps you previously had "International" as an Opp Type.    You clear the check box in the field Active and use a Record Picker Report to prevent Users from being able to use that in the future.

Your Opportunity records that were International still are and will not have the annoying red color to them.   

The goal is not to make anything cumbersome for the developer.  Our goal is to make it easy on the User.

From the diagram, the check box is your field [Active]  in the Opp Type Table.

You should try this with a quick test application.   Make a new application with just the two table described above.  Use the real names from your current application so that it is a relevant test.

In the parent table, which I called Opp Type, make a report that shows all records where Active = TRUE

Use that report as the Record Picker for your Users in the form for the table I called Opportunity.  Again use your own names.

Then test it by adding some records.

Then change the Active box and see how the User Experience changes when they create more records.

Another thought I had with this solution is I also lose the function for the user to be able to select more than one option - they can only select one option in the record picker. Whereas my previous field is multi-select and they can select more than one option. 

That depends on your business rules.   If your logic allows for more than one answer to be true, then you need a Many to Many

The Architecture is designed to support the business case.