We've experienced both no problem and an unhappy surprise when checking in late.
We had one stay at the YC where we arrived at 1:50am for a 5 night stay. The CM at check took forever at the computer & with our magic bands. We finally got on our way & headed to our room, it was about as far from the lobby as you could get without being considered a Beach Club guest... lol. Our MBs would not open the door, hike back to the desk where a different CM says it's probably still linked to your other room. I explain that we have just arrived at WDW and there has been no other room yet this trip. He looks confused for a split second and I ask if we had been assigned a different room which somehow had been changed. I then ask if there is anything closer to the lobby. The answer, nothing available due to the Villans Weekend happening at HS and the Resort is fully booked. There had been another room attached to our file. This was born out by our checkout statement, it showed room 3177 for our arrival night and room 4236 for the other 4 nights.
Our MBs kept reverting back to the original room daily the entire stay and we spent a good chunk of time at the desk getting them reset, they'd work for everything but our room door.
And to add insult to injury - I went to the desk with my statement on our last day & asked where 3177 is located - 3rd floor over the back entrance with a full view of the lagoon and SAB. A far cry from our standard roof top view in 4236. We had been upgraded & lost it! We didn't realize it until that last day.
(it did work out for future trips - I've requested to be close to the lobby & added "near room 3177 if possible" and gotten my request!)