Hmm, sorry I got sidetracked and didn't get back to you earlier.

You're going to need ProntoProEdit NG, and Marantz RC3200 Edit (which can work with NCFs using normal Pronto hex). (I recommend rebooting after installing both.)

Open the PCF ProntoProEdit NG and find the device/pages with the buttons you need. Double click on the button, and then double-click on "Learnt IR Code" line. If it doesn't say that, then you can't do the conversion. You'll get a window with an "IR Code" box near the bottom. If the code doesn't start with 0000 then you can't do the conversion. Copy this entire code to the clipboard (select and then CTRL-C).

Now open Marantz RC3200 Edit. Create a new file. Create a new device. Add a new page. Create a small button. Double-click on the button. Click on "Edit IR". Paste the code you copied (CTRL-V).

Repeat that for all commands you need to copy.

Now save the new file to an easy-to-access location and exit both programs.

Now you need to open the NCF file you made in RC3200 Edit as a ZIP file, using some sort of software such as WinRAR or WinZip. Note that you may find this easier to do if you rename it to ".zip".

Edit the comment section. Change the RC3200 specific comment from:

Type:001
Version:001.000

to the Boston specific version:

Type:006
Version:001.000

Note that I had trouble doing this using the NCF created by RC3200 Edit; WinRAR kept complaining it was corrupt whenever I tried to make a change. So I ended up decompressing its contents to a directory, then re-saving that as a new ZIP, manually adding the comment, and renaming to .NCF.

Exit, and load the NCF file in FreedomEdit. Note that you will likely want to repair install FreedomEdit to make it the default NCF editor again.