Warning: The R400, R600 and R700 series of presenters are attack vectors and considered harmful. While Heise made an article that detailed that Logitech would exchange the receivers, it did actually not. They sent out a pair of incompatible C-U0014 receivers which could not be paired with R-R0004 presenters and then stopped their program, claiming only to exchange the presenter if it was under warranty, which is a security nightmare (I just tried to get the correct receiver, but Maven M. from Logitech wanted to have the receipt for the module which I obviously do not have anymore). In other words: The hardware is extremely vulnerable, Logitech accepts that it is like that but does not want to get this fixed, so I can only recommend to dispose of the presenter line and do not buy from Logitech anymore. Here is the security write up with the proof of concept to that attack: https://seclists.org/fulldisclosure/2016/Oct/60
To pair an old R400 presenter with a new dongle (or vice versa), try to get the right dongle for your presenter version first:
As stated here, there are two versions of dongles for the presenters - and they are not interchangable:
"There are two versions of presenter receivers that can't be interchanged.
C-U0005
Use the C-U0005 receiver with these presenters:
Wireless Presenter R400 with M/N = R-R0004
Professional Presenter R700 with M/N = R-R0006
Professional Presenter R800 with M/N = R-R0003
C-U0014
Use the C-U0014 receiver with these presenters:
Wireless Presenter R400 with M/N = R-R0008
Professional Presenter R700 with M/N = R-R0010
Professional Presenter R800 with M/N = R-R0009
You can find the model number (M/N) of your presenter inside the battery compartment."
After that, download the Logitech Presenter Connection Software from here (Sorry, only Windows...), start the file and unzip the content.
Update again to this post from 2015 now in 2021: Logitech removed the links from its website, but you still can find the file on its ftp server: ftp://ftp.logitech.com/pub/techsupport/mouse/presenter_connection_zipped.exe ;).
Start the file and unzip the content.
Then, connect your dongle, find the logitech_presenter_connection.exe and start it. After that, the software will ask you to power up your presenter while holding down the to the left and to the right keys of the presenter. 3+ seconds after powering up and holding down the keys, you can release the keys, turn off the presenter again and click Ok in the software. Power on your presenter again and see if it works, if not - try the procedure again.
Update (2019): Had to update the links as they were from 2015 and have changed due to Logitech deciding to changing their design (Thanks Michael!). Also please note the R400, R700 and R800 presenters are considered insecure and the dongles are now replaced by Logitech: https://www.heise.de/security/meldung/Angreifbare-Logitech-Presenter-Hersteller-tauscht-gefaehrliche-USB-Empfaenger-aus-4423627.html
Update (2021): Had to update the download link again, thanks Christopher for asking. But I guess you need to start the software with admin rights (maybe even Win XP, Win 7 "emulation"?), I could not pair my second dongle right now, but the battery is also nearly flat, so that should be an issue.... the software as what I had back then... Maybe it helps some one 🙂