If you have only merged one Individual record from the main tree with one Individual in the dirty tree, then all the other Individual records and Family records from both trees still exist. So the merged Individual has two sets of parents, and two spouses, and has a Marriage event for both spouses. They just all happen to have the same names, dates, places, etc, but the records will have different Record Id.
Please clarify what your objective is?
I am guessing that if the 'dirty' tree is now 'clean' then you want to amalgamate that entire sub-tree into your main tree, which involves a lot of merging of many records.
If my guess is right then it will be better to do a file merge.
First, just to be on the safe side, use
File > Project Window > More Tasks > Copy Project to create a working copy Project.
Use
File > Import/Export > Export > GEDCOM File... and export the whole sub-tree with Media.
In the working copy Project delete that whole sub-tree.
Now use
File > Merge/Compare File... and import that exported GEDCOM file.
That should automatically sync all the matching Individuals.
Then work through each tab Individuals, Families, Sources, Places, etc, etc, and check all records are merged correctly.
See FHUG Knowledge Base
Merge/Compare File for further advice.
Repeat the sub-tree export, delete and merge for each sub-tree.
You may have to clean up duplicate &/or unlinked Media files afterwards.
Finally, delete the original main Project and rename the working copy Project as required.