Before I suggest a method, it may be best for you to create a copy of your database to test with to make sure it does what you want.
'File->Save a Copy' then give it a name and open that new copy.
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Need a little more information.
What Edition of CB do you have? (Express, Pro or Archive)
(I will assume Pro or Archive as they have Advanced Find)
1) For the Issues removed, has the QTY value been set to 0?
2) When removing box number from the Custom Field, do you want ALL of that number removed?
For example, if a Find for Custom Field = 'AC' would you want all issues found to have it removed or would there be some issue you do not want it removed?
3) If the above answer is 'Yes I want all occurrences of box number 'AC' to be removed, would be true for all the various box numbers?
If the answers are 'Yes all the QTY have been set to 0, this should be possible.
If the answers are 'No all the Qty have not been set to 0 but the various Box number values would ALL be removed, this should be possible.
If the answers are 'No all the Qty have not been set to 0 but the various Box number values would NOT ALL be removed, then it may not be possible (or at least, difficult).
A) All Qty have been set to 0:
Advanced Find Where: I.Qty = 0 AND I.Custom Field 1 (or whatever the field name is) IN ('x1', 'x2', 'x3, (etc. until you list all the various box number values) )
B) All specific box number values are to be deleted:
I.Custom Field 1 (or whatever the field name is) IN ('x1', 'x2', 'x3, (etc. until you list all the various box number values) )
C) Qty = 1 but only some of the box number values would be deleted:
The same Advanced Find for 'B' would work but you would have to manually select the ones to be deleted
For A and B, after the Find Result rows are displayed:
Select All rows.
Right-Click and select Quick Change from the pop-up menu.
Select Change drop-down
When the result rows are displayed, Select All rows, right-click and select the Custom Field.
Leave the 'TO:' box blank
Click Make Changes
Let me know if you need any clarification.