I have an independent claim in my application for software patent that could be rejected on grounds like "abstract idea". There are a few dependent claims with limitations that hopefully pass the bar. Still I want to keep independent claim in case if somebody will try to patent it and I won't have any recourse because it is less limiting. So assume my independent claim is rejected, but dependent claims are granted, does it mean that the independent claim will be excluded from the grant? Then somebody would be able to patent it if his reviewer is more lenient.
I will come to the point that how the patent is examined, see examiner first check application for NOVELTY and finds some document he comes back with few references as you said its already disclosed or abstract idea. This leads to NON FINAL REJECTION you try to amend it with dependent claim and he comes with OBVIOUSNESS based FINAL REJECTION you file RCE request (good fee) with your reply and hopefully he comes with response which requires more amendment and that make you case more weaker and costly.
it has been always great to make it fair and wise that you put your best foot forward. Put claim you feel novel its going to create good case and at least two good chances to convince examiner.
Now since you have disclosed 'matter' it in your specification it cant be used as such to get a patent on. yes it becomes prior art.
If you're working with a patent lawyer, you should speak with her or him about this because this is the kind of thing that patent lawyers are quite good at navigating.
Here is the way to think about patent claims: The independent claim must stand on its own. The claim must be novel, not obvious, useful, and must satisfy the section 101 requirements for patentable subject matter. Dependent claims incorporate all of the limitations of the independent claim from which they depend, so if the independent claim is patentable, the dependent claims should also be patentable. However, a dependent claim cannot depend from a non-patentable independent claim.
So if your independent claim is rejected, but the limitations in a dependent claim would overcome the reasons for rejection (for example, the independent claim is obvious, but the dependent claim adds a non-obvious element), you will probably get an office action from the USPTO saying basically that if you rewrite the independent claim to incorporate the limitations of the dependent claim, they'll allow it to issue.
With regard to the other part of your question, once you have filed for a patent on a claim, it becomes "prior art" to subsequently filed patent applications and it will prevent them from issuing (assuming no errors in the examination process).