systemctl stop kodi.service
mv /storage/.kodi/userdata/guisettings.xml /storage/.kodi/userdata/guisettings.old
systemctl start kodi.service
this will "lose" current Kodi GUI config things but you can always reverse the process. Does this solve the issue? I've tested subtitle positioning in a VM install of LE and it works fine so I'm wondering if things have gotten messed up somewhere.
It would help if you described the problem you are trying to solve and shared the patch you are trying to use (and where it came from)?
PuTTY is an SSH client, not a file transfer client.
If you need the ability to resume transfers use rsync or an SFTP software (FileZilla, WinSCP, Transmit, etc.)
Sync Playback to Display tells Kodi to use the display clock for sync purposes, but passthrough audio requires VideoPlayer to use media for clock sync (else you are modifying the source, which is not true passthrough) so if you enable SP2D passthrough is automatically disabled. This is different from Jarvis where SP2D is effectively broken but a collection of hacky things kind-of works. Krypton fixes things, so in summary: Krypton != Jarvis.
The forum "search" function is the magnifying glass icon top-right on the screen.
The lack of documentation is bad, but also a good n00b filter. Over the years we noticed those who will be successful in their attempts to create custom builds (and have some dev skills) figure out the build system quickly and get on with things relatively unaided as it works logically and already contains a wealth of prior-art which serves as the instruction manual. Those who have no skills or aptitude for the task will continue to ask in forums/IRC for howto guides. It's fairly easy to spot the first group from the questions asked. Carry on 
systemctl stop kodi.service
rm -rf /storage/.kodi/temp
systemctl start kodi.serviceThat normally frees up a chunk of space. If you need more you're looking to prune thumbnail caches which is a little more advanced.
Create a diff patch of your changes from the root folder of build.LibreELEC-RPi2.arm*/linux-4.9 and place in projects/RPi2/patches/linux/linux-002-mystuff.patch or in packages/linux/patches/ with a suitable sequence number (patches are applied in order) then re-run the build command. The linux package will be cleaned and rebuilt with the patch applied. If this fixes something that others would benefit we'd also encourage you to PR the patch to our git repo so it can be included until it works its way into mainline kernel.
Hard to guess what the root issue is but something add-on related would be my guess. If you took a backup in OE before starting it will be quickest to create a new SD card and then selectively restore things of importance. If you didn't and you are only seeing the Jarvis splash screen you can SSH into the box and rename /storage/.kodi to /storage/.kodi-old - then once the system is up you can stop Kodi and selectively restore things as required. If you are seeing the first LE boot splash and the box is fully rebooting that won't be possible and you'll need to remove the SD card and mount the storage partition in Linux to rename .kodi to .kodi-old before doing the same selective restore. You can also try clean install and restoring the backup, but that probably gets you back to the same boot-loop point.
Krypton disables installation from zip unless you explicitly enable support in Kodi settings. This is a new function designed to make people think twice before installing pirate add-ons. There are no known issues installing other skins. If you believe there to be an issue please enable debug and component http logging then clean boot. Once rebooted demonstrate the problem and run "cat /storage/.kodi/temp/kodi.log | paste" or use the log file submit option in the settings add-on to create a sprunge.us URL to share the log file. No log = No problem.
Nice. Welcome to the 21st century
Fix is merged and will appear in next release. I'll mention the wakeup issue to others .. it's not part of the OS that I understand.
Please test LibreELEC-Generic.x86_64-7.90.010.tar which contains an updated version of atvclient and report back here with results. I no longer test this package with AppleTVs so it got missed in the move to Krypton.
Nope. I got back from from vacation this afternoon and will look at the build issue sometime tomorrow .. and by the time that's done we'll be releasing something with Kodi 17.0-RC1 so I'll probably skip creating a 7.90.010 build and just run with that.
Update to LibreELEC-Generic.x86_64-7.90.010.tar and then run "dmesg | paste" and share the URL again. The build has the ath10k driver enabled; it is unlikely to give working wireless as-is but I can see the firmware load failure messages. Thanks.
Repositories are add-ons that are installed from a zip file like any other Kodi add-on. Most people who publish a repo for public consumption will also provide a zip to install the repo. NB: @vpeter's add-on was cleaned-up a little and is now in our main add-on repo as "Touchscreen" .. so no need to install a repo.
Install Hyperion from our add-on repo. Use our version of HyperCon (look in our wiki) to configure it.