Refresh and Analyze starts by charging the cells using the same termination methods as the standard charge mode. So, it really doesn't matter if the cells are charged or not when you start refresh and analyze. If they are charged, they should terminate in less time, rest, then discharge, etc. If they are not, they will simply take longer to charge.
Break-in is different in that it is a timed charge at a low rate. Break-in mode requires you to set the cell capacity, then the charger uses a C/10 charge rate timed for 16 hours. (Eneloops at C/10 = 200mA.) Charging at C/10 is not as efficient as charging at higher rates, that is why it is timed for 16 hours rather than 10 or 11. NiMH cell are much more tolerant of overcharging at C/10 so starting a break-in cycle with cells that are already charged shouldn't harm them. But, that just goes against the grain with me. I always discharge cells before using break-in mode...I just feel better about it.
My NiMH cell care method:
I run a break-in on all new cells (discharged first) then run a break-in once a year. As I understand it, break-in help to distribute the electrolyte in the cell.
I charge Eneloops at 1000mA as needed. If a cell hasn't been discharged enough over the last three months in normal use (such as in TV remotes) I cycle it, 400mA discharge, 1000mA charge, and consider it good for the next three months. I happen to use cycle for this but refresh and analyze would work just as well.
If I'm not using in a cell, I discharge it, charge it at 1000mA for about 10 minutes (so it has some charge) and place it in ziplock bag in the refrigerator for storage. When I want to use it, or every three to six months, I take the bag out of the refrigerator and allow it to come up to room temperature over night, and charge it. If it is going back into storage, discharge, charge 10 minutes at 1000mA and back into the ziplock and the refrigerator.
I have had good results with this method. I remember the first NiMH batteries that I got years ago. Charge them up one week later they were dead whether you used them or not.