I think all is good just that the reporting of (an older version of) lasinfo confuses you. For all extended_classifications of 32 or higher the legacy classification was not just set to zero but also counted as zero in the histogram. I believe that this was fixed in the later versions of LAStools. Below a similar example:
:: creating a LAS 1.4 file
las2las -i ..\data\fusa.laz -set_point_type 6 -o fusa14.laz
:: this is how it looks now
lasinfo -i fusa14.laz
lasinfo (170915) report for fusa14.laz
reporting all LAS header entries:
file signature: 'LASF'
file source ID: 0
global_encoding: 0
project ID GUID data 1-4: 00000000-0000-0000-0000-000000000000
version major.minor: 1.4
system identifier: 'LAStools (c) by rapidlasso GmbH'
generating software: 'las2las (version 170915)'
file creation day/year: 40/2010
header size: 375
offset to point data: 469
number var. length records: 1
point data format: 6
point data record length: 30
number of point records: 0
number of points by return: 0 0 0 0 0
scale factor x y z: 0.01 0.01 0.01
offset x y z: 0 0 0
min x y z: 277750.00 6122250.00 42.21
max x y z: 277999.99 6122499.99 64.35
start of waveform data packet record: 0
start of first extended variable length record: 0
number of extended_variable length records: 0
extended number of point records: 277573
extended number of points by return: 263413 13879 281 0 0 0 0 0 0 0 0 0 0 0 0
variable length header record 1 of 1:
reserved 43707
user ID 'LASF_Projection'
record ID 34735
length after header 40
description 'by LAStools of Martin Isenburg'
GeoKeyDirectoryTag version 1.1.0 number of keys 4
key 1024 tiff_tag_location 0 count 1 value_offset 1 - GTModelTypeGeoKey: ModelTypeProjected
key 3072 tiff_tag_location 0 count 1 value_offset 32754 - ProjectedCSTypeGeoKey: WGS 84 / UTM 54S
key 3076 tiff_tag_location 0 count 1 value_offset 9001 - ProjLinearUnitsGeoKey: Linear_Meter
key 4099 tiff_tag_location 0 count 1 value_offset 9001 - VerticalUnitsGeoKey: Linear_Meter
LASzip compression (version 3.1r0 c3 50000): POINT14 3
reporting minimum and maximum for all LAS point record entries ...
X 27775000 27799999
Y 612225000 612249999
Z 4221 6435
intensity 10 62293
return_number 1 3
number_of_returns 1 3
edge_of_flight_line 0 0
scan_direction_flag 0 0
classification 1 6
scan_angle_rank 79 103
user_data 0 197
point_source_ID 1 1
gps_time 5880.963028 5886.739738
extended_return_number 1 3
extended_number_of_returns 1 3
extended_classification 1 6
extended_scan_angle 13167 17167
extended_scanner_channel 0 0
number of first returns: 263413
number of intermediate returns: 283
number of last returns: 263370
number of single returns: 249493
overview over extended number of returns of given pulse: 249493 27232 848 0 0 0 0 0 0 0 0 0 0 0 0
histogram of classification of points:
17553 unclassified (1)
180868 ground (2)
37030 high vegetation (5)
42122 building (6)
:: modify the LAS file
las2las -i fusa14.laz ^
-change_extended_classification_from_to 6 40 ^
-change_extended_classification_from_to 1 42 ^
-set_extended_overlap_flag 1 ^
-set_extended_scanner_channel 2 ^
-odix _mod -olaz
:: this is how it looks now after the modifications
lasinfo -i fusa14_mod.laz
lasinfo (170915) report for fusa14_mod.laz
reporting all LAS header entries:
file signature: 'LASF'
file source ID: 0
global_encoding: 0
project ID GUID data 1-4: 00000000-0000-0000-0000-000000000000
version major.minor: 1.4
system identifier: 'LAStools (c) by rapidlasso GmbH'
generating software: 'las2las (version 170915)'
file creation day/year: 40/2010
header size: 375
offset to point data: 469
number var. length records: 1
point data format: 6
point data record length: 30
number of point records: 0
number of points by return: 0 0 0 0 0
scale factor x y z: 0.01 0.01 0.01
offset x y z: 0 0 0
min x y z: 277750.00 6122250.00 42.21
max x y z: 277999.99 6122499.99 64.35
start of waveform data packet record: 0
start of first extended variable length record: 0
number of extended_variable length records: 0
extended number of point records: 277573
extended number of points by return: 263413 13879 281 0 0 0 0 0 0 0 0 0 0 0 0
variable length header record 1 of 1:
reserved 43707
user ID 'LASF_Projection'
record ID 34735
length after header 40
description 'by LAStools of Martin Isenburg'
GeoKeyDirectoryTag version 1.1.0 number of keys 4
key 1024 tiff_tag_location 0 count 1 value_offset 1 - GTModelTypeGeoKey: ModelTypeProjected
key 3072 tiff_tag_location 0 count 1 value_offset 32754 - ProjectedCSTypeGeoKey: WGS 84 / UTM 54S
key 3076 tiff_tag_location 0 count 1 value_offset 9001 - ProjLinearUnitsGeoKey: Linear_Meter
key 4099 tiff_tag_location 0 count 1 value_offset 9001 - VerticalUnitsGeoKey: Linear_Meter
LASzip compression (version 3.1r0 c3 50000): POINT14 3
reporting minimum and maximum for all LAS point record entries ...
X 27775000 27799999
Y 612225000 612249999
Z 4221 6435
intensity 10 62293
return_number 1 3
number_of_returns 1 3
edge_of_flight_line 0 0
scan_direction_flag 0 0
classification 0 5
scan_angle_rank 79 103
user_data 0 197
point_source_ID 1 1
gps_time 5880.963028 5886.739738
extended_return_number 1 3
extended_number_of_returns 1 3
extended_classification 2 42
extended_scan_angle 13167 17167
extended_scanner_channel 2 2
number of first returns: 263413
number of intermediate returns: 283
number of last returns: 263370
number of single returns: 249493
overview over extended number of returns of given pulse: 249493 27232 848 0 0 0 0 0 0 0 0 0 0 0 0
histogram of classification of points:
180868 ground (2)
37030 high vegetation (5)
+-> flagged as extended overlap: 277573
histogram of extended classification of points:
42122 extended classification (40)
17553 extended classification (42)