When I import images from my Canon cameras using EOS Utility I have it automatically change the filenames to include the date the photo was taken as well as the 4-digit image number assigned by the camera. I also automatically create a folder for each date that images on the card were shot and images are placed in each folder based on the date they were shot.
Operating systems and storage capacities are a lot different than they were 15 years ago when the naming conventions and file structures for the DCIM folder under the Design rules for Camera File Systems were being ironed out. I've never experienced a problem with files named something like 201611150001.cr2. After editing and exporting them they're even longer: 201611150001LR.jpg (low resolution version), 201611150001HR.jpg (high resolution version), 201611150001HRhdrmc.jpg (High resolution HDR monochrome version), etc.
Once images are transferred to the computer and backed up at least two other places the cards are formatted in camera before being used again. I've got the cameras set so the image numbers continue where they left off, even after reformatting the cards. So if the last image of a previous shoot was IMG_6875 I can put any of my various cards in the camera, format the card, and the next image I take will be named IMG_6876.
One thing that may cause the image numbers to be assigned out of sequence is if you swap cards and then put a card you used earlier back in the camera without reformatting it. Putting a card with images taken using one EOS camera stored on it into another EOS camera and recording images to it can also cause gaps in the image numbers.
A word about memory card best practices.
I've shot over a quarter-million frames since going digital in 2008. I have yet to lose a single image due to a corrupt card issue. I have accidentally deleted a few and recovered them with varying degrees of success. I attribute this to several practices that I follow.
Every camera maker recommends using the camera to reformat the memory card periodically. Doing so helps reduce the risk of data loss because each time a card is reformatted bad sectors can be mapped out of the card's directory. Most memory cards contain more memory than they show. The reserve capacity is used to replace bad sectors when they are detected by the card's on-board memory controller. Deleting some but not all data on a card and then shooting more images increases the risk of corruption with flash memory cards. It can also impact the speed at which your camera can write to the card if the file has to be fragmented over several sectors because it is larger than the space cleared by the image you erased. The increased risk is very slight, but it is there.
- Always turn off the camera and be sure the card access light has stopped blinking before opening the memory card slot cover.
- Only remove the card from the camera when absolutely necessary (i.e. the card is full and I'm still shooting a session). This includes transferring images to the computer using the camera, rather than a card reader. I understand not everyone agrees with this preference, but I'd rather wear my batteries out a little sooner than risk losing images due to card insertion errors. Voltage is just voltage, but no two images are the same. If you do use a card reader, be sure to use the OS "eject" command before removing a hot swappable card. For CF cards best practice is to power down the computer before removing the card from the reader. Although the USB reader may be hot swappable, the CF card standard does not include such a requirement.
- If your camera uses CF cards, be very careful to make sure the pins in the card slot are lined up properly with the holes on your card.
- Replace your card(s) periodically. Wear leveling helps extend the life of flash memory cards, but they do wear out eventually. If a card starts acting flaky at all, it's time to replace it NOW.