MySQL Workbench model/source synchronize issue
MySql Workbench is powerful, but not perfect.

Some time in similar case, I've done the following to resolve the problem:


create a blank project
require a model update FROM db source
then I'll reapply the mod. 


Often this happen if you just change a 'comma' [a small thing] in the db without sync it with the model, and then you change another 'comma' in the model. MySql Workbench goes crazy often as db increases in complexity and table number, but I think it's a very good product.