This is quite old and hasn't been fixed:
NC updater 15.0.2 still fails on Delete old files (core/shipped.json is not available)

1. I had to add "'maintenance' => false," to config.php -- otherwise the updater wouln't make it past the Backupstep. (Why don't we add some smart interactive choices?)
2. Nearly every step has a parsing error. (Why can't the updater wait a bit more?!!)
3. Updater doesn't make it past the Delete old files step because of missing core/shipped.json

I see that I am not the only one. The Updater index.php needs some MAJOR overhaul.

Snipped from updater log. (domain name changed)
2019-04-11T21:06:48+0000 DQkRuGYe3N [info] rollbackChanges("9")
2019-04-11T21:06:48+0000 DQkRuGYe3N [info] unlink .step
2019-04-11T21:06:48+0000 DQkRuGYe3N [info] rollbackChanges - step >= 7
2019-04-11T21:06:48+0000 DQkRuGYe3N [info] end of rollbackChanges()
2019-04-11T21:06:48+0000 3q1nnwSQwU [info] request to updater
2019-04-11T21:06:48+0000 3q1nnwSQwU [info] currentStep()
2019-04-11T21:06:48+0000 3q1nnwSQwU [info] POST request for step "9"
2019-04-11T21:06:49+0000 3q1nnwSQwU [info] startStep("9")
2019-04-11T21:06:49+0000 3q1nnwSQwU [info] deleteOldFiles()
2019-04-11T21:06:49+0000 3q1nnwSQwU [error] POST request failed with other exception
2019-04-11T21:06:49+0000 3q1nnwSQwU [error] Exception: Exception
Message: core/shipped.json is not available
Code:0
Trace:
#0 /customers/2/3/6/mydomain.de/httpd.www/nextcloud/updater/index.php(1337): Updater->deleteOldFiles()
#1 {main}
File:/customers/2/3/6/mydomain.de/httpd.www/nextcloud/updater/index.php
Line:891