*** This bug is a duplicate of bug 1897754 ***
    https://bugs.launchpad.net/bugs/1897754

This looks like a timing issue related to the recent changes in the U20.04.01.
A simple fix which works for me is to delay the start of NextCloud for several 
seconds (5 in my case), by adding
X-GNOME-Autostart-Delay=5
to the ~/.config/autostart/Nextcloud.desktop file.

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https://bugs.launchpad.net/bugs/1846944

Title:
  Nextcloud client app indicator icon not visible in 19.10 Eoan Beta

Status in gnome-shell-extension-appindicator package in Ubuntu:
  Confirmed

Bug description:
  When running the Nextcloud Client (flatpak or PPA) in Eoan Beta, its
  app indicator icon is never displayed in the notification area. Other
  apps sch as Steam and Skype have their indicator icons displayed fine.

  Output from the command line when running the flatpak produces the
  following error:

  Qt: Session management error: None of the authentication protocols
  specified are supported

  I can duplicate this issue 100% of the time.

  ProblemType: Bug
  DistroRelease: Ubuntu 19.10
  Package: gnome-shell-extension-appindicator 30-1
  ProcVersionSignature: Ubuntu 5.3.0-13.14-generic 5.3.0
  Uname: Linux 5.3.0-13-generic x86_64
  NonfreeKernelModules: zfs zunicode zavl icp zcommon znvpair
  ApportVersion: 2.20.11-0ubuntu7
  Architecture: amd64
  CurrentDesktop: ubuntu:GNOME
  Date: Sun Oct  6 13:35:44 2019
  InstallationDate: Installed on 2019-09-23 (12 days ago)
  InstallationMedia: Ubuntu 19.04 "Disco Dingo" - Release amd64 (20190416)
  PackageArchitecture: all
  SourcePackage: gnome-shell-extension-appindicator
  UpgradeStatus: Upgraded to eoan on 2019-09-27 (8 days ago)

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