I use Nikon transfer from within ViewNX2 on both my laptop and my work PC. I have file renaming systems all set up and it does not try to transfer files that have previously been loaded on each respective machine. It may be slow but I get reliable and consistent file naming and directory sorting across different machines.
I have it set to leave the original image files on the card so I can download them later to an archive disk on a second home PC.
On my Laptop, even though it has USB3 ports, I find that using the built-in SD card reader is faster than using the camera with supplied USB3 cable. But I have never lost a file with either method and not with previous cameras or computers either. There is not much risk of damage by removing and replacing SD cards regularly.....but there is a risk of damaging pins in the camera's and reader's card slots if you are not gentle with your CF cards.
I allow all the images to accumulate on the card and once full I erase all and reformat it. This works for me because I do not do huge shoots. Maybe 100 to 200 shots in a day at most.....and I keep an empty 16Gb CF card in the 2nd slot on the D800 for emergencies.
BTW - if the original files have merely been "erased" from the card then they are still there provided no new files have been written to the card since erasing them. Erasing generally just erases the entries in the card's file allocation table but the original data is undisturbed until it is overwritten by new files. Various card recovery software products can be used to recover any files that have not been overwritten. However if the card was reformatted- then they are likely gone.