Possible steps you could take:
1. Create a new Flag, call it say Split
2. Backup your project/gedcom - for reference I'll call it Master
3. Go through the project and mark/tick all those who you want to split from Master with the new Split flag ticked.
4. Create a new custom query that show all individuals that have Split ticked - call it say Marked
5. Create another query that shows all individuals that do NOT have Split ticked - call it say UnMarked
6. Those two queries should show which Individuals you have or have not marked and the number of rows for each should add up to your original Indi count
7. Backup your Master gedcom again.
8. Goto 'master'.fhdata and make a copy of the Master gedcom - Ctrl-C
9. Paste the copy Ctrl-V and rename the gedcom Copy as say MarkedMaster.ged
10. Paste again and rename the Copy as say UnMarkedMaster.ged
11. Effectively at this stage you will have 3 gedcoms : Master, Marked and UnMarked or whatever you decided to call them.
12. Load MarkedMaster.ged and run split tree helper and select the third option, Delete all records Not Found by the query below, then select your Marked query from the dropdown. Pick any other options you need, and click Delete
13. Your MarkedMaster gedcom should now have only those that you marked with the flag Split
14. Load UnMarkedMaster.ged and run split tree helper and select the second option, Delete all records Found by the query below, then select your Marked query from the dropdown. Pick any other options you need, and click Delete
15. Your UnMarkedMaster.ged should now have only those records that were not marked with the Split flag.
I did something similar to this a few years ago when I split a large gedom into two seperate entities. Double check my logic before you start.