Changes have been made in Git (master):

commit 753923287843ce7885570df2574db4c60be66f72
Author: Jan Schneider <jan@horde.org>
Date:   Wed Feb 22 14:33:15 2017 +0100

     [jan] Fix removing custom permssions when removing a user or 
group from a share (Bug #14578).

  framework/Share/lib/Horde/Share/Object.php | 12 ++----------
  framework/Share/package.xml                |  4 ++--
  2 files changed, 4 insertions(+), 12 deletions(-)

http://github.com/horde/horde/commit/753923287843ce7885570df2574db4c60be66f72

I'm sorry, I mixed things up when I wrote down the bug report.

The actual problem arises when horde-remove-user-data is executed for 
the user that has got "Delegate" permissions on the share, not the 
share owner.

Example:
mysql> select * from kronolith_sharesng_users where share_id=101638;
+----------+----------+--------+--------+--------+---------+-----------+
| share_id | user_uid | perm_2 | perm_4 | perm_8 | perm_16 | perm_1024 |
+----------+----------+--------+--------+--------+---------+-----------+
|   101638 | bbeispie |      1 |      1 |      1 |       1 |         1 |
|   101638 | jwahnes  |      1 |      1 |      1 |       0 |         0 |
+----------+----------+--------+--------+--------+---------+-----------+

$ horde-remove-user-data bbeispie
Removing data of user(s):
   bbeispie

Are you sure you want to remove user data?
     (y) Yes
     (n) No

Ihre Auswahl [n]: y
[   OK   ] bbeispie: Data removed.

mysql> select * from kronolith_sharesng_users where share_id=101638;
+----------+----------+--------+--------+--------+---------+-----------+
| share_id | user_uid | perm_2 | perm_4 | perm_8 | perm_16 | perm_1024 |
+----------+----------+--------+--------+--------+---------+-----------+
|   101638 | bbeispie |      0 |      0 |      0 |       0 |         1 |
|   101638 | jwahnes  |      1 |      1 |      1 |       0 |         0 |
+----------+----------+--------+--------+--------+---------+-----------+

I cannot reproduce this, and I don't see how this could happen either. 
In _removeShare() 
https://github.com/horde/horde/blob/master/framework/Share/lib/Horde/Share/Sql.php#L791 we completely delete the rows from the share tables that are associated with the calendars that we are removing. We don't resent permission flags 
individually.

A calender which is shared with another user, giving out  "Delegate" 
permissions (perm_1024), is not properly deleted when the user that 
this calendar belongs to has its data deleted through 
horde-remove-user-data.

Instead, upon horde-remove-user-data, the other permissions on this 
particular entry in the kronolith_sharesng_users table are set to zero 
(e.g. perm_8 is set to 0), but the perm_1024 column remains at the 
previous value "1". This is with the sharesng SQL driver at least, I 
have not tried using other backends.