Of course you always have the option to reset the ordering to the original position in the Db's table (same documentation link posted above) :
Automatically set the field order
With an existing project, it can be tedious to set the field order on every entity by hand. LLBLGen Pro offers the ability to set the field order based on the ordinal order of the mapped target fields in the table / view. How LLBLGen Pro does this depends on how you want to work.
For working database-first, this is done during a catalog refresh if the project property ResetFieldOrderBasedOnTargetOrderAtRefresh is set to true (default is false). When reverse engineering, new entities created through reverse engineering will only get their fields ordered after the ordinal ordering of the fields of the tables/views they're mapped on if the project property UseCustomFieldOrderingOnNewElements is set to true (false by default).
For working model-first, this is done when a new entity is defined and if the project property UseCustomFieldOrderingOnNewElements is set to true (default is false). Fields added to a new entity will automatically get a field order (the last known field index + 1) if that setting is set to true. This works regardless of how you add the field: in the entity editor or through QuickModel or for example through adding a relationship and it will create a foreign key field in the entity.
Another option is to refactor your method calls using a smart VSNet regex Find/Replace operation. A trivial example would be (not tested):
Find: {.}order{.}.FetchUsingPK({[0-9]+}, {[0-9]+})
Replace: \1order\2.FetchUsingPK(\4, \3)
Above example would find all entity variables that contains the word "order" and switch their numeric PK parameters.