How big is your input flowdir grid (pixel height x pixel width)?
If I'm not wrong (I calculated height and width after extent information of my raster, already projected) this raster has 8779 pixel-height by 7904 pixel-width (I subtracted top - bottom, and right - left in extent information, and then divided both by pixel size...was that correct?).
Flow accumulaton can take an extreemly long time to run on large grids. I have had some flow accumulation process take a week to run on a fast machine.
After I read your response on Friday I left in 2 machines the tool running, came back after the weekend and both are still working, one lost connection to the server (now is back connected, and continue with the process) and the other says "updating flow accumulation" and arc map is not appearing/displaying the raster, only the status bar shows work in progress ("Updating Flow Accumulation"). I will leave for some more time, as you suggested.
However, I've done same tool/process with same raster source but for different regions and -I would say- such similar large area size, and it worked very well, I have delineated my drainage areas/polygons for other 2 nearby regions. Yes, it took time (a few hours) for those previous, this situation appeared for this last region.
The larger the flow accumulation you have in your data, the longer the tool will take to run. So, for example, it will take much longer to run for a grid mostly composed of a large single basin that drains to one point (like the Amazone River) than a grid of the same size that has many smaller basins that drain radially outwards from the center (like Mt. Kilimanjaro).
one lost connection to the server (now is back connected, and continue with the process)
You might be referring a license server here, but...
not problem with license, I've checked that too.
One of the largest performance enhancements you can make with any ArcGIS tool is to processes the data using your local hard drive(s). That is, don't try to run these processes from data stored on a network.
In both cases, rasters are placed on main drive (C:/).
What it's interesting is that in both cases the Flow Accumulation status is shown as "in progress", and on the background the open ArcMap says: Not responding.
Since the message in the status bar is: UPDATING FLOW ACCUMULATION, that means ArcMap is in processing and that is why "IS NOT RESPONDING"?
This time I've not even try to touch this process and it still on...since last Friday.
Also, I assume you ran the Fill tool on your input DEM (before you made your flow directions grid), correct?
It seems like moving from 90m to 20m shouldn't increase processing time this exponentially.
It will because the number of cells increases by the square of the cell size. So if you ere processing 10,000 cells going from 90 to 20m increases the number of cells to process by a factor of more than 20!