Fos example,you migrated a Treecko from Ruby to Diamond.Will Treecko still be in Ruby?
No. The Treecko will be moved FOREVER into Diamond out of Ruby.
If I'm understanding your question right then the answer is no...... Example A Umbreon can be obtained in Platinum, but its original region was Jhoto. I can still migrate that Umbreon to my Pokemon Black even though its in the Shinnoh Region.