This isn't a terribly risky thing in and of itself. You can revert things back pretty easily. The big risk is that an error in setting up any relationships or differences between your two hopefully identical Episode tables. That could have unintended consequences for your data if records link differently than before.
Always make back up copies of your files during development.
Always make frequent back up copies of your files during development
Examine both Episode tables thoroughly. Check their field definitions and the the data to confirm that they are truly identical and resolve any differences.
The most basic step is pretty simple.
Open one of the files and go to Manage | Database | Relationships.
Select an Episodes Table Occurrence box by clicking it.
Use the button to the left of the percent magnification box to find all table occurrences with this same data source table. (If there is more than one, make them all a unique color.)
Double click each such table occurrence box and use Add Filemaker Source to point it at the Episode table in the other file.
Now both files share the same Episode table.
Click OK and test to make sure everything works.
You can physically merge the two tables by importing the tables from one file to another, but it can be a lot of work and you have to be very meticulous about recreating value lists, relationships and scripts. You can import scripts and copy and paste layouts but if there's any real complexity to your design, this can take a lot of time and you risk introducing errors into your design. And for all that you don't really gain any major advantages.
Filemaker Advanced's Database Design Report is well worth the extra $$ for this task.
FMMigrator has been mentioned in this forum. I haven't used it myself, but I'd check it out if I had such a "file merge" to do.