Hm, that could be a reason. I've never done this myself, no idea if aTc or others have tried that yet.
It shouldn't touch anything other than the partition it booted from.
When you get to the desktop it will probe for removable disks and mount them, (like when you insert an sd card in another slot, or attach a usb device), and it just mounts whatever is on the emmc as part of that, it doesn't get written to by anything.
My direct experience was:
Loaded the OS flash to eMMC. Booted from it. It worked 100% over ~4 reboots.
Created an OS card for the SD slot. Booted from it. It worked 100% over ~3 reboots.
Removed the card from the SD slot.
Booted from the eMMC. OS is now 'rotten'. Things that worked now don't, etc.
The only 'change' that I can point to is having booted from the SD card.
There are a lot of differences between the OS image used in the eMMC OS and the SD card OS. Boot is ext2 vs ext4. Whether the left shoulder shift works or not during the Welcome script. Likely more, but I'm not planning to reflash the eMMC again tonight. I need a break from that, so I'm sticking with the left SD slot booting for now.
There are clearly differences between the two, though. From my poking around, the SD boot feels like the superior version. Which one would be seen as the 'more current' one? Is there a path/plan to get them back in sync?
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New topic: USB charging ports oddities.
OS used: SD card
'Smart' USB 3.1 hub with a 2.5A charging port capable of negotiated voltage/current.
'Dumb' USB 2.0 hub with a 2A charging port.
USB volt/amp measurement device put in between to test draw.
microUSB charging/serial port plugged into either charger, draws 0.45A
microUSB 3.0 wide port plugged in with cable (fat 3.0 or narrow 2.0) to either charger, draws ~1.7A (a bit variable)
If the microUSB charging/serial port is plugged in and drawing 0.45A and a device (OTG hub, card reader, etc) is plugged into the mciroUSB 3.0 wide port, charging through the charging/serial port stops and current draw on the charging/serial port drops to 0.00A AND the device on the microUSB 3.0 port is inactive.
If the mciroUSB charging/serial port is empty and an OTG device is plugged into the USB 3.0 wide port, then the OTG hub, card reader, etc gets power, works as normal and devices show up in the file system (good).
I haven't figured out a configuration where I can get the charging/serial narrow USB to draw more than 0.45A. Isn't this one supposed to be our main charging port?
Charging through the microUSB 3.0 wide port seems to work quite well using fat 3.0 or narrow 2.0 cables.
Right now it seems that I can either supply power to the Pyra OR use the USB 3.0 OTG functionality while draining the battery.
The reverse case works fine. I can supply power via the USB 3.0 wide port and use the serial communications from the charging/serial port without issue.
How I envisioned it working:
Hub is powered via a 3.5A wall plug.
USB charging/serial port draws main power (up to 2+A) from a charging port (no data) on my hub.
Hub USB 3.0 host port plugs into the USB 3.0 wide connector on the Pyra.
Both plugs in use simultaneously. One draws power, the other hosts the USB 3.0 hub allowing keyboard, data devices, ethernet, etc.
Is this a known issue?