Connectivity errors found - open scratchconnect_low.tga and scratchconnect_high.tga (in the exe's working directory) to see
t:\branches\shogun2\modders\common\tooldatabuilder\source\CampaignMapData/CampaignRegions.cpp(908) : TOOLDATABUILDER::REGIONS::build_connectivity
CONNECTIVITY ERRORS... and how to deal with them.
If there have been earlier errors or warnings related to clipping, resolve these.
Make sure that edges in the inaccessible areas - the shapes formed by merging the mountains and the inaccessible ground types - always intersect properly with region edges.
Ie, the intersection point must be between the two end points, not at a vertex - so they should not cross at a vertex, or share a vertex.
If this doesn't solve it, the next likely issue is that you have a region with a hole, and an inaccessible area (mountain/ground type) overlapping it.
The clipping code does not handle holes - the internal outlines are not clipped.
Assuming the hole is a lake or similar, then it's a no-go area already. There are two ways to deal with it.
If the mountain is entirely within a region, you can extend the mountain to include the lake (and remove the lake from the regions layer).
Alternatively you can burn the whole mountain and lake into the regions layer as nogo_land.
If the mountain extends over a region boundary, you can cheat and extend the lake to that boundary, even along a thin sliver.
This would mean cutting a very simple thing into the map and still having the mountain layer used.