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Q1 CheckConvexity issue: Exposed floor "88ADEF" is certainly non-convex. The Shading Calculation Method is PolygonClipping (default), while your Solar Distribution choice is FullExteriorWithReflections. These should not trigger non-convex warnings IMHO. Maybe linked to this open issue. If you really want to get to the bottom of this, break up the floor surface into 3x distinct rectangular surfaces.

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Q2 Mismatched interzone surfaces & areas: You have a first set of 3x problematic surfaces (stripped-down IDF inputs):

B5C9E7,              !- Name
Wall,                !- Surface Type
U_2D01,              !- Outside Boundary Condition Object
6.057, 6.630,  6.600
6.057, 6.630,  3.400
6.057, 9.880,  3.400
6.057, 9.880,  6.600

U_2D01,              !- Name
Wall,                !- Surface Type
B5C9E7,              !- Outside Boundary Condition Object
6.057, 8.130, 6.600
6.057, 8.130, 3.400
6.057, 6.630, 3.400
6.057, 6.630, 6.600

1F431C,              !- Name
Wall,                !- Surface Type
B5C9E7,              !- Outside Boundary Condition Object
6.057, 9.880, 6.600
6.057, 9.880, 3.400
6.057, 8.130, 3.400
6.057, 8.130, 6.600

... mismatched vertices + "B5C9E7" is referenced 2x. It looks like it should be broken into 2x wall surfaces: one facing "U_2D01", the other facing "1F431C".

Another pair of problematic surfaces:

7F857D,                  !- Name
Wall,                    !- Surface Type
C05674,                  !- Outside Boundary Condition Object
 6.057, 6.630, 6.600
 6.057, 6.630, 3.400
11.057, 6.630, 3.400
11.057, 6.630, 6.600

C05674,                  !- Name
Wall,                    !- Surface Type
7F857D,                  !- Outside Boundary Condition Object
11.057, 6.630, 6.600
11.057, 6.630, 3.400
 3.057, 6.630, 3.400
 3.057, 6.630, 6.600

... vertices don't line up. I suspect a need to break up "C05674", and an orphaned/missing surface somewhere.

Q3 Mismatched construction layers with interzone surfaces:

559937,                          !- Name
Ceiling,                         !- Surface Type
DasarAtap,                       !- Construction Name
C680B1,                          !- Outside Boundary Condition Object

C680B1,                          !- Name
Floor,                           !- Surface Type
Interior Floor,                  !- Construction Name
559937,                          !- Outside Boundary Condition Object

DasarAtap,                       !- Name
ID GypsumBoard 12 mm;            !- Outside Layer

Interior Floor,                  !- Name
ID GypsumBoard 12 mm,            !- Outside Layer
F05 Ceiling air space resistance,!- Layer 2
M15 120mm heavyweight concrete,  !- Layer 3
ID Plaster-Wall,                 !- Layer 4
ID Ceramic;                      !- Layer 5

... constructions of coupled interzone surfaces need to match (same layers, yet in reverse order if asymmetrical).