Sync service on Linux starting as different user?

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Hi there! I am hoping someone can help me as I am a bit lost.

I have setup Resilio Sync on Linux (Raspbian to be exact) but now I think I have done something wrong and it keeps trying to start Sync as a different user. I have about 7 folders synced with 15gb so I really don't want to start again.

It all started when I began trying to get the service to run at boot. It was working fine prior to this point.

I tried to edit the service file via the following
sudo nano /lib/systemd/system/resilio-sync.service
and changed the User & Group variables to pi. I also changed the WantedBy to

I edited /usr/lib/systemd/user/resilio-sync.service to also have WantedBy to

This was the last point I could see the folders when I checked by opening the gui.

I tried a crontab by:
sudo crontab -e
And adding:
@reboot rslsync

I think I tried a different function in here to add it to the systemd as another way to try and get it to load on boot, but I can't get my terminal to recall it for some reason.

I found a guide that said this may be an issue as I initially set it up under the rslsync user. I changed it to pi after install as I am syncing the files on a USB and rslsync did not have the correct permissions to access the media. So I ran the following:

systemctl --user disable resilio-sync
sudo systemctl disable resilio-sync
systemctl --user enable resilio-sync

I found a guide that said when running on headless to always force it to run as the current user to use -
sudo loginctl enable-linger pi

Now the service does start at boot (which I have checked by opening the gui directly after boot), but it doesn't show my folders - it loads into the setup box asking to set a username and password. 

Have I destroyed my setup or have I just made a faux par by making it load as a different user? Thanks in advance for the help, I am a bit stressed as I was getting this setup before I depart on a vacation.

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