Hi, I have got a message popped up that there are updates for me, but it disappeared before i could click. How can I retrieve this message again?
Restart the IDE and let it sit for a while. Or you can do Sketch > Include Library > Manage libraries and Tools > Board > Boards Manager... and select Type: updatable.
Sometimes those updates can cause problems. Often the Arduino board updates are not tested for backwards compatibility with older IDE versions. For example, the latest Arduino AVR Boards is not compatible with any IDE version older than 1.6.9 but they will still happily tell you to update, thereby breaking your IDE. In general I'd say it's better to update to the latest IDE version, though that may also subject you to some bugs. Some of the 3rd party boards developers will do a better job at backwards compatibility testing.
Library updates are generally safer. There are certain cases where updating a library can break things but of course there is a reason why they released a new version of that library: fix bugs, add features, improve performance, etc.