The change in symbol and comment handling since SYSWIN is the result of a move towards IEC 1131 standards.The standard insists on guaranteed correct placement of symbols and comments.
SYSWIN does not delete comments but provides no guarantee that they are correctly positioned when merged with an uploaded program.
It is in an attempt to always guarantee correct placement that causes CX-Programmer to delete existing comment and local symbol files.
So if a program is changed only in the PLC, remerging becomes difficult. This is a particular problem for those older PLCs that do not accept comment (CMT) place marker instructions.
Where possible, it is good practice to only download, or compare and correct a program, rather than upload it.

It is possible to upload programs with comments from any PLC that can store comments in the form of formatted file memory or memory cards.
Additionally those PLCs that use Comment Instructions (CMT) can have the uploaded program merged with stored comments using the "Transfer To File" and "Transfer From File" commands.
Thus many PLCs, other than those with a memory card, can display comments after an upload.
That some PLCs do not store comments is a hardware limitation not a software one.
Global Symbols are not deleted during an upload, Local symbols are.