Your library entries will transition between Desktop and Reference Manager with minimal issues. However, the new in -text citation tool, Mendeley Cite, uses a different Microsoft Word function than the legacy Cite-O-Matic tool.
If you currently have manuscripts in progress with inserted intext citations from Desktop and the Cite-O-Matic tool, you may wish to continue using those Mendeley products until that manuscript is completed.
You can load Mendeley Reference Manager on your local computer and install the Mendeley Cite tool (plug in) into your MS Word without installing Mendeley's Cite-O-Matic tool, and begin new manuscripts. However, you will need to be careful to remember which tool you are using with each manuscript!
Current versions of the Mendeley Cite plugin for Microsoft Word can now convert citations inserted with the legacy Cite-O-Matic tool. Please first make and save a copy of your document as a backup, because no tool is perfect. More information is available on the Mendeley support website.
If you currently use the Mendeley Desktop software to manage your library and group materials, you will need to click on the synchronize button, shown above, to ensure that your data is completely synchronized with your Mendeley cloud storage.
Watch the bottom of your Desktop software window (on a Windows computer) to see when the synchronize process is complete. (What does this look like on a mac??)
After you have synchronized your Mendeley Desktop, you may close the Desktop software window.
Now you can install the new Mendeley Reference Manager software (add link) and log into your account. All of your files/folders (aka collections)/groups/data/annotations should be loaded into Reference Manager when it automatically synchronizes.
In Reference Manager, each time you update an entry or make an annotation, it will automatically synchronize with your cloud storage, unless you opt to work offline (link to elsevier's tips about working offline).
If you are going to uninstall Mendeley Desktop completely, you will want to first use the Mendeley Desktop, Tools Menu to uninstall the Word tool, Mendeley Cite-O-Matic. You do not need to uninstall these in order to install and begin using Mendeley Reference Manager and Cite.