Hi Samuel:
That problem occurs with at least 50% of conversions for me.
One solution is to add a leading digit to all Department codes so that "000" becomes "1000", "001" becomes "1001" etc. But it's not a very popular solution because it requires more keystrokes; I've never had anyone make that choice, though I suppose there might be growing organizations where a 4-digit Department makes sense.
The other choice is to replace the leading zero with another digit. For a conversion currently underway, they were able to use the digit "1" because the 100-199 series wasn't in use yet (that was a lucky break). in another they went with "9" because the "0" series Departments were all administrative and it didn't affect the rank-and-file staff members.
Maybe after 20 years they could see this as an opportunity to do a more extensive COA restructuring?