Plugins of map mods often make changes to the worldspace records. Make sure to finalize the load order and make sure that the last plugin to overwrite the worldspace records (with maps) to contain all desired changes before generating LOD. DynDOLOD uses the records from the winning plugins when creating the DynDOLOD and Occlusion plugins. Do not disable any plugins when generating LOD, simply follow the Generation Instructions for the current load order as usual. The DynDOLOD and Occlusion plugins will automatically contain the correct overwrite records from the winning (map mod or patch) plugin and the DynDOLOD and Occlusion plugins can be sorted last as usual.
Instructions to overwrite the DynDOLOD or Occlusion plugins or to modify any of the generated plugins, LOD meshes or LOD textures after they have been generated for the finalized load order are categorically wrong. DynDOLOD is a patcher to automate these things. Disabling plugins is a troubleshooting step and not a fix. Use the official DynDOLOD support forum for qualified advice in case of problems or questions to have any issues properly discussed and addressed.
Terrain LOD meshes filenames are of the form ..Data\Meshes\Terrain\[Worldspace name]\[Worldspace name].[LOD Level].[X].[Y].BTR. For example..Data\Meshes\Terrain\Tamriel\Tamriel.32.0.0.BTR. In this case make sure the meshes of the map mod overwrite any other terrain LOD meshes, including the ones generated by xLODGen. Since DynDOLOD does not generate terrain LOD meshes or textures, there is no conflict with TexGen output or DynDOLOD output.
Object LOD meshes filenames are of the form ..Data\Meshes\Terrain\[Worldspace name]\Objects\[Worldspace name].[LOD Level].[X].[Y].BTO. For example ..Data\Meshes\Terrain\Tamriel\Objects\Tamriel.32.0.0.BTO.
LOD Level 32 object LOD meshes typically do not exist in a vanilla game, so by default DynDOLOD generates object LOD meshes for LOD level 4, 8 and 16. Which means, if a map mod contains LOD level 32 object LOD meshes, there is no conflict with default TexGen output or default DynDOLOD output. See Ultra Tree LOD - Trees on the Map how to generate object LOD level 32. In the case that DynDOLOD is used to generate object LOD level 32 files specifically, they should overwrite the map mod files to take effect.
In case a map mod contains LOD level 16 object LOD files and it is really desired to use them, then the meshes of the map mod need to overwrite the DynDOLOD output. The LOD level 16 object LOD files is also seen in the normal distance views, so there may be artifacts from the map visible.
In case the map mod ships with its assets in a BSA, extract all the LOD files from it. Sort the map mod with a high enough priority in the load order, so that its loose files overwrite other terrain LOD or object LOD files as required. Alternatively, delete or hide the generated terrain LOD or object LOD files, so they do not overwrite the files of the map mod in its BSA.
For quicker testing, consider generating object LOD and nothing else for Tamriel only. Once everything works and look OK, generate the LOD patch for the load order and all worldspaces with the desired options.
If Seasons of Skyrim is used - which requires seasonal LOD files - manually copy any terrain LOD or object LOD files from the map mod to the different seasonal filenames *.[SPR|SUM|AUT|WIN].[BTR|BTO], so that a version of the map files exists for every season. For example ..Data\Meshes\Terrain\Tamriel\Objects\Tamriel.32.0.0.WIN.BTO.
See Seasons for more information.