[UPDATE]I just upload a new alternative version of the boot disk, named "Boot_df1.adf". As you can probably figure out by the name, you can use this boot disk, to make all transfers using the second external drive, instead of the internal!
By doing so, you can leave permenantly the boot disk on internal drive, and change disks on external drive, so whenever a problem occurs you just reset amiga without needing to insert the boot disk again!

Also,i had some minor bugs fixed in both 32bit and 64bit versions of adf transfer program:
- Choosing a read only adf image to transfer, doesn't cause "sticking" on copying this same image. So no need to manually delete the "temp.adf" file anymore (the workaround used so far)
- No need to restart application to change i/o address of parallel port. This might also fix some issues regarding the configuration file of dosbox being "read only"
As always, you can find the new boot disk and versions of the program
here.