Hi,
I faced the same problem converting from MSAccess. SQLyog copy routine doesn't copies indexes and autoincremets (at least I found it works so with Access). So I have got mySQL table with INT field instead of auto-increment. When I tried to convert this field to auto-inc, values have been renumbering sequentally as I have gaps in numbering.
One solution I see is to index this field as UNIQUE – in this case values aren't changing. But if you will add new rows you should fill this field by yourself (i.e. using MAX(..)+1).