The problem here is to maintain file identity when the camera starts duplicating former filenames.
Ways to maintain file identity are: (1) Keep files from subsequent rounds of 1000 in separate folders and rely on the folder name to maintain file identity, or (2) rename files so you can relocate them freely.
If you're renaming files, when should you do it: (1) As part of the process of moving them to the computer, or (2) as a separate step after they're on the computer. (I think Thom Hogan recommends the former in his "Complete Guide to the Nikon D70".)
If you're renaming, some forms of the new filename are: (1) prefix the DSC name with the date using some file transfer software; or (2) rename DSC_xxxx to DSE_xxxx, DSFxxxx, etc.; or (3) rename DSC_xxxx to DSC_1xxxx, DSC_2xxxx, etc. (There are, of course, zillions of others.)
How to rename: (1) Let the software that moves the files to the computer do it, or (2) use the command line Rename function (this can do the DSE_xxxx option), or (3) use a specialized renaming program like "THE Rename" (found in the other thread that EmekaU mentioned; this can do the DSC_1xxxx option, or just about any other kind of name change you can dream up).
At this point the command line rename option seems best for me. I'll just transfer new files to a folder like ...\New, and run a command line batch file against the files in that folder, implementing ren DSC_
.jpg DSE_ .jpg, then move the files to wherever I want them to live.
Thanks to everyone for the helpful ideas. You helped me focus on options and get clear on what best fits my work pattern. And now I don't think there is A best practice; there may be a best practice for YOU, but it depends on how you like to work.
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