(Class
   "BusinessClassesRoot"
   "<NONE>"
   TRUE    ->this one was interpreted as persistent / transient
   FALSE  -> this one as abstract / concrete
   ""
   ""
   "persistence=persistent,_Boldify.autoCreated=True,Bold.TableName=<Prefix>_OBJECT"   -> then there is TV persistence that has precedence

No check this:

(Class
   "TransientAbstractSuperClass"   -> name implies transient abstract
   "BusinessClassesRoot"
   TRUE   -> WRONG
   TRUE  -> Correct
   ""
   ""
   "_BoldInternal.toolId=4E6E06670175,persistence=persistent  ->WRONG

(Class
   "TransientSubClass"      -> name implies transient 
   "TransientAbstractSuperClass"
   TRUE   -> WRONG
   FALSE  ->Correct
   ""
   ""
   "_BoldInternal.toolId=4E6E066701C3,persistence=persistent"   -> WRONG

You see? Can you check the files? I used this one: ModelerTest-FromBold-boldified-flattened.bld.txt

(Class

  "TransientAbstractSuperClass"

  "BusinessClassesRoot"

      FALSE

      TRUE

      ""

      ""

      "_BoldInternal.toolId=4E6E06670175,persistence=transient,Bold.FileName=trans_includename.inc,Bold.TableMapping=Children"

...

(Class

    "TransientSubClass"

    "TransientAbstractSuperClass"

        FALSE

        FALSE

        ""

        ""

        "_BoldInternal.toolId=4E6E066701C3,persistence=transient"

...