HI @pone,
I do not see why not, but it'd not be an easy task...
That being said, this is one of the many reasons why we built RESCRIPt, see the paper here. In fact, Figure 5 highlights the differences in taxonomic annotation that you refer to.
Each database can differ because they can make use of a different taxonomic schema, and might make different decisions about curating the data / taxonomy. I'd highly recommend reading these articles (there are more but these are a good start):