It is undoubtedly that something is wrong with your merging logic, however your task is quite interesting and this is one of the possible ways it can be solved.
I took your structure and made an assumption that none of the rows in your table is fully filled, i.e. either first three columns are filled (struct_left) or last three (struct_right). This is how I feel it from your screenshots.
REPORT z_sections.
TYPES:
BEGIN OF struct_left, " left structure
LEFTDAMAGED TYPE c LENGTH 1,
LEFTDAMAGEDDESC TYPE c LENGTH 3,
LEFTDAMAGEDDESCT TYPE c LENGTH 30,
END OF struct_left,
BEGIN OF struct_right, " right structure
RIGHTDAMAGED TYPE c LENGTH 1,
RIGHTDAMAGEDDESC TYPE c LENGTH 3,
RIGHTDAMAGEDDESCT TYPE c LENGTH 30,
END OF STRUCT_right.
TYPES BEGIN OF ty_table.
INCLUDE TYPE struct_left.
INCLUDE TYPE struct_right.
TYPES END OF ty_table.
DATA: lt_current_table TYPE TABLE OF ty_table INITIAL SIZE 100,
ls_current_table LIKE LINE OF lt_current_table,
i TYPE i.
FIELD-SYMBOLS: <fld> TYPE clike.
DATA: r_random TYPE REF TO cl_abap_random_packed,
seed TYPE i.
seed = cl_abap_random=>seed( ).
CALL METHOD cl_abap_random_packed=>create
EXPORTING
seed = seed
min = -999999999999999
max = 999999999999999
RECEIVING
prng = r_random.
DEFINE randomize. " filling row with random data
ASSIGN COMPONENT &1 OF STRUCTURE &2 TO <fld>.
<fld> = r_random->get_next( ).
&1 = &1 + 1.
ASSIGN COMPONENT &1 OF STRUCTURE &2 TO <fld>.
<fld> = r_random->get_next( ).
&1 = &1 + 1.
ASSIGN COMPONENT &1 OF STRUCTURE &2 TO <fld>.
<fld> = r_random->get_next( ).
END-OF-DEFINITION.
START-OF-SELECTION.
* filling table with random stuff
DO 100 TIMES.
CLEAR ls_current_table.
IF sy-index MOD 3 = 0.
i = 1.
randomize i ls_current_table.
ELSE.
i = 4.
randomize i ls_current_table.
ENDIF.
APPEND ls_current_table TO lt_current_table.
ENDDO.
DATA: ls_left TYPE struct_left,
ls_right TYPE struct_right.
DATA lt_new LIKE lt_current_table.
* collapsing table
LOOP AT lt_current_table ASSIGNING FIELD-SYMBOL(<fs_current>) WHERE leftdamaged IS NOT INITIAL.
DELETE lt_current_table WHERE leftdamaged IS INITIAL AND leftdamageddesc IS INITIAL AND leftdamageddesct IS INITIAL AND
rightdamaged IS INITIAL AND rightdamageddesc IS INITIAL AND rightdamageddesct IS INITIAL. " remove empty lines
MOVE-CORRESPONDING <fs_current> TO ls_left.
READ TABLE lt_current_table ASSIGNING FIELD-SYMBOL(<fs_right>) WITH KEY leftdamaged = ''.
IF <fs_right> IS ASSIGNED.
MOVE-CORRESPONDING <fs_right> TO ls_right.
CLEAR: <fs_right>.
ENDIF.
CLEAR: <fs_current>.
IF ls_left IS NOT INITIAL AND ls_right IS NOT INITIAL.
CLEAR: ls_current_table.
MOVE-CORRESPONDING ls_left TO ls_current_table.
MOVE-CORRESPONDING ls_right TO ls_current_table.
APPEND ls_current_table TO lt_new.
CLEAR: ls_left, ls_right.
ENDIF.
ENDLOOP.