I've just done this with a Lumia 830, I downsized to a 32GB SD card to keep app data for planned retirement of the phone in December (since the total app data exceeds the 16GB built in storage). I had a 128GB card in the phone, which is going in a 950/XL when it's released.
Move what data you can from the internal storage to the new SD card using storage spaces, then swap the cards back and move data from the old card to the internal storage. Keep swapping the cards round as necessary until you've got all the data you want from your old card.
In my case, I've had zero issues - the games I had installed on my 128GB card have transferred, via the internal memory, to the new card and run perfectly without data loss.
Using the file explorer on a Windows PC to directly transfer the data from one card to the other may not work - I assume application settings might play up, plus the phone may want to format the new card when you 1st insert it into the phone.
Having said that, I did move the map data directly as for WP8.1 you can't move map data to the SD card anymore with the retirement of the Lumia storage app. I moved the map data directly with file explorer on my desktop without issue and the phone still saves new maps to the SD card.
Mileage may vary, but I had no issues. Obviously can't guarantee there won't be issues but in my case I had none.
Also note that, in my case, some apps used far less space when on the internal memory, only to take far more when on the SD card.
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