one more thing, might be related, it doesn't show master item as a part of item name in Configuration tab:

unlinked and cleared all items from host. Reattached template. Error gone away. Weird.

ok, it now happens for other items from prototypes. They are UNSUPPORTED and are not updated(not becoming supported no matter what) even though i corrected preprocessing and the should work now.
vso please report it separately as server issue, thanks!

Reported once again as ZBX-13115 and reproduced in 3.4.4

This is an issue on the server side. master_itemid remains empty in the case described in ZBX-13115.

Is there a known workaround to fix this condition manually somehow, without loosing the item history?

vso server will rediscover items and fix links after update, it's possible to do manually but it's quite cumbersome work.

Fixed in development branch:
svn://svn.zabbix.com/branches/dev/ZBX-12661

Successfully tested

Fixed in:

• pre-3.4.6rc1 76619
• pre-4.0.0alpha2 (trunk) 76622

fixed Low-level discovery of dependent items not working after being edited and resulting in undefined offset error or foreign key constraint violation