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There are applications that are widely used out there (just think of PHP, MySQL, etc...). What would happen if the organisations behind them pull this software back into closed source?
On what grounds can these companies bring (parts of) Open Source projects into closed source?
For example, parts of MySQL now under management of Oracle, have become close source. How is this justified and isn't this against the OS licences?
An open source license is a grant from the copyright holder to someone else, giving them additional rights. If I give you the rights to version 2 of my work, I don't have to give you rights to use version 3 of my work, because it's mine. If version 2 is GPL, version 3 can be BSD licensed, closed source, or only available to Martians, that's up to me.
Now, if I have code in my work that belongs to other people that they have given to me under the GPL, I can't unilaterally change the license, because that would involve someone else's stuff. But other licenses, such as BSD, would allow that.
The concept of Copyleft is relevant to your question - for non copyleft or permissive open source licenses, the fact that a derived work can disappear behind a closed source license is considered to be a feature, not a bug.
Both sets of free software licences offer the same freedoms in terms of how the software can be used, studied, and privately modified. A major difference is that when the software is being redistributed (either modified or unmodified), permissive licences permit the redistributor to restrict access to the modified source code, while copyleft licenses do not allow this restriction.
First, the most general case:
All common open source licenses permit any legal entity to make a private copy and to use it for their private, internal use. Some common open source license (Copyleft/Free) impose restrictions on other uses, such as distributing a derived work or running a service on the internet using the derived work.
You framed the question as 'on what grounds,' but really the question is, 'what are permitted uses of the source code under the terms by which it was licensed.'
Now, a more specific case. If an entity owns the copyright of a work, and chooses to publish it under an open source license, that entity can change its mind. This does not change the status of copies already out there. So, for example, if Oracle owns the copyright of MySQL, Oracle is entitled to stop publishing MySQL under a FLOSS license, and distribute new copies in binary only -- or even not distribute it at all. That does not change the status of the previous releases.
