ImageMosaic store was created for raster layer. Everything OK.
Now additional .sid files were added so new shape was generated manually with
gdaltindex command. When new shapefile is created I go to layer configuration in GeoServer and press "Compute from data" but BBox does not change (I know for sure it now has larger BBox). If I do a GeoServer restart and then press "Compute from data" for this layer only then BBox gets recalculated. That is an issue one.
Even when I successfully restart GeoServer and recalculate BBox issue two persists: when opening GWC GUI for layer caching I see that BBox still has the old values. To fix this I have to go to
../data/gwc-layers/LayerInfoImpl-xxxx and manually change coordinates.