How can I merge two folders in Windows?

I would recommend using the free Microsoft RichCopy. RichCopy is essentially an updated GUI and backend for Microsoft's older Robocopy. This utility works very well and is highly configurable. It has the ability to continue if an error is encountered so as not to abort the overall copy process. One of its more notable strengths is the ability to very easily allocate resources (assign multiple process threads, cache size, etc..) to control the overall copy process in a very granular fashion. I use this tool often to merge gigabytes of source data into a single folder. It will also output a command line string if you would prefer that. The tool in unsupported by Microsoft but over the years I have had no issues with it's day to day use.

Key Features of RichCopy

1. More powerful, faster and stable than than any other file copying tool.
2. Create several profiles to assign special settings with a specific profile.
3. Copy files from multiple and different locations and save in a single destination.
4. Filter the files based on the date, time and choose to either copy or opt those files.
5. Being on GUI, supports command lines.
6. Suspend and resume file copy at any time.

You can read further details with additional information here.

You can download RichCopy here

WinMerge has the ability to compare two folders. The compare can recursively process folders. The compare will tell you which files are identical, different, and exist in only one folder or the other. It also has functions that will move files from one side of the comparison to the other for you.

Unless you want to combine files, you can likely find a way to use Robocopy (see link for usage examples).