Estimating Database cleanup

We have recently upgraded to 16.11 SQL Estimating and after working to get the Export to Job Cost set up have found that there are some "ghost" job cost phase values that have been there for a very long time but need to be changed.  In order to be able to do the export to Job Cost, the cost code formatting in Estimating had to be changed. (one used a period and the other a dash!)  I have gone into the db and made the corrections for all of the JC Phases that are applicable.  However, the ones that are not applicable still have the wrong format and it seems that sometimes for an item a JC category may be applicable so they will just add it on the estimate.  When this happens of course the export  gives an error due to the wrong format of the cost code. I am being told that when the db items were first created, that an "Inherit JC Phase" was done and that is how the "ghost" something is in the ones that do not have Applicable checked.

My question is, is there any reason to not go ahead and make all of the categories applicable and change them to the correct job cost code?  What is the reasoning for not having all 5 of the categories applicable and a jc phase(cost code) defined for all? 

Thanks in advance!