The reason for doing this isn't clear (at least, to me), and I don't see it as any kind of security trick because the problem it creates is trivial to resolve. All this does is overwrite the offset part of the immediately preceding STA instruction with a different value (from $0100 to $0020). The net result is that the S19 created will have duplicate data for the same address possibly causing problems with certain programmers that will choke on this.
Depending on how smart the programmer software is this may confuse it. Some programmers will load the whole file in memory, create a 'final' memory image of what to burn to the device and then start the burning process. Others, will burn as they read the file, and they will complain when they try to reprogram an already programmed location.
The solution is simple.
Make a copy of the S19 file and edit it with a plain text editor. Find the S1 record that contains this offset and go write 0020 over the 0100 (of the STA $100,x instruction). This will still have an overwrite in the S19 file but your programmer may not complain as the overwriting value is the same as the previous one. If it does, more work is needed. You must remove the extra two bytes from wherever they appear (normally next S19 record, unless the S19 file has been re-sorted).
This should be very easy if you're lucky enough that the two bytes (of the DW directive) are in an S1 record all by themselves (just delete the whole S1 line). If not, you need to also edit the S1 record's length byte after you delete the four hex digits from the S19 ASCII file.
In any case, if your programmer refuses to process the edited S19 file due to CRC errors (instead of simply giving a warning and proceeding), then you'll also need to update the CRC of the related S1 record(s). This is the final byte.
For details about the exact format of the S19 file you can have a look here: SREC (file format) - Wikipedia, the free encyclopedia
(If you still can't figure it out, I could help with the conversion if you send me the S19 file and the above snippet from the LST file.
You should probably check the S19 file with this tool from P&E (S_TEST) found here: P&E Microcomputer Systems in case there are more than one occurrence of this issue in your file.
Hope this helps.