As a general rule, I leave Name Auto Correct turned off. Even if the corruption problems have been corrected, it still adds significant overhead to your development process and it doesn't work the way you think it does. However, when I need to make bulk changes and I want the help, I turn it on. But, before you do that, make sure to read carefully the attached document because as I said, it doesn't work the way you think it does. In particular, changes are not actually propagated until the target object is opened. So if you change a column name, the change is logged but nothing else changes. Only if you open each form/report/query/macro will the change be propagated. Where people get into trouble (and I'm sure NAC gets confused) is when there are layers of changes to apply. So, I make changes to one table at a time and open all objects that use the table. Then go back and do the next one. The doc contains a link to where I got it originally.
To make this work for you, you will need to go back to a one file .accdb by importing back all the linked tables. That is the only way Access can propagate changes. You can't change linked tables from the FE and when you change them in the BE, Access has no clue what FE should be changed. So - merge them back. It's a lot of trouble to go through so make sure it will be worth your time. If the BE is SQL Server, the problem is even worse because importing the tables one at a time won't import the relationships and PKs and Indexes, you will need to recreate all of them.
If your changes are sporadic, don't bother with NAC. Make the changes to the BE. Then open EVERY FE object and fix the errors as they are reported. And in any case, NAC cannot change code so you are on your own there. It also doesn't change calculated fields in queries so you'll have to ferret those out yourself. There is a global change product that does a better job but you still have the BE/FE issue.