New merged content that is merged using Mator's zMerge program marks the new esps with a HEDR version of 1.70.  This can be problematic if the merge contains record ids with the new esl format, since the "HEDR - Header" version dictates how the plugin uses those records.  Therefor it is important to change the "HEDR - Header" version number so the plugin formids are displayed and read correctly and don't unintentionally overwrite base game formids they shouldn't.

Note:  This does not apply to Skyrim LE users.

Changing the number is easily done using SSEedit/Xedit. 
Open the new merged plugin with Xedit.
In the left panel you will see all the loaded plugins.  Right clicking on the merged plugin will open a window on the right displaying that plugins information.
At the top of the right panel, you will see the Record Header and below that, you will see the HEDR - Header.
Beside version, you will see the HEDR version number of 1.700000.  Double click on the number and change it to read 1.71.  Press enter.  The four following 0 will be added automatically.  X out of Xedit and make sure the box to save the plugin is checked.  Click ok, and you are done.