Probably I have figured out the reason for this abstract behavior. After applying the workaround stated above, everything was fine. Then I restarted RTC and I found that everything was working well.
But just to check the cause of above problem, I closed two of the projects in my eclipse workspace. Each of these two projects are connected to two different repository workspaces and third project (which is my current project) is connected to third repository workspace. All the repository workspaces are on the same jazz server. After closing the two projects in eclipse workspace when I restarted the RTC again, the same 'unreachable' repository workspace problem was there.
This same condition was also there when I encountered the problem earlier in the day which I forgot to mention in the above post. I had closed two of my projects in my eclipse workspace.
I want someone from jazz team to please comment on this issue or is this some jazz configuration issue.

- Ankur

I guess the 2nd post which I did is not the reason of the problem. Because I faced the problem even when I didnt closed the projects in eclipse workspace.
But this time I restarted RTC and in 'Pending changes' view, it asked me to connect to some repository workspace and choose it to be my desired workspace and everything is again fine. (This is same as option of 'load repository workspace...' from 'Pending changes' view.) So this is better workaround than 'unload-load' workaround.
Also one of my repository connection is to localhost jazz server which is set to automatic login. But usually when I start RTC, local server is not running, so it shows not connected to localhost. Can this be somehow cause of the problem ?
This problem is somewhat of random nature.

- Ankur

I am expecting some replies from jazz SCM team, atleast what does that error message means?

Requesting someone to please reply on this problem

Hi Heather

Thanks for looking into this problem.

Just to make some points clear, I neither deleted repository connection of Jazz Server A nor did I deleted my repository worksapces on Jazz Server A. Every time when I start RTC, I am also able to log into the jazz server A and can do all the operations. But it shows my Repository workspaces on A as unreachable in pending change view. So I do some 'workaround' every time so that atleast it starts showing me that this repository workspace is linked to my local eclipse project and shows me pending changes and allows me to check in & deliver my changes.

But in order to know the cause of problem I just tried some of the options and found that it shows me error when I try to load the component from my local repository workspace. (Although the same component is already loaded in my eclipse workspace, but trying to load it again should not result in any errors.) This is error shown to me

CRJAZ0215I Item not found: com.ibm.team.scm.common.internal.impl.WorkspaceHandleImpl@67d467d4 (stateId: <unset>, itemId: [UUID _3MTQkPZ3Ed2VCsYzYSkn2Q], origin: com.ibm.team.repository.client.internal.TeamRepository@2eec2eec, immutable: <unset>)

Please note that this error is shown even after I apply the workaround and be able to checkin the code in the component. I believe it won't be easy for me to reproduce these step, but doesn't this error give any clue about the problem.

When you started up, the Pending changes view attempted to provide you with information about incoming and outgoing changes for all the workspaces you have loaded. However because it could not log into the jazz servers or because the workspace was deleted, it was not able to get the information it needs for these workspaces.It tells you about them because you may have contents from them loaded but makes it clear that they are unreachable and so you can not undo changes, checkin changes etc.
You should in the pending changes view unload the workspaces you deleted from the jazz servers.

I didn't have any contents loaded from any other repository workspaces which I deleted.

For remaining workspaces you are interested in to be reachable, you must be logged into the jazz server that they are defined on.

As I told earlier I am logged into the server already and infact after applying the workaround I am able to reach to the repository workspace also.

For workaronud I follow these steps:
From 'Pending changes' View menu select 'Load Repository workspace...' option. It opens a window showing me the my repository workspaces on jazz server A, I choose on of them, click OK. Next it asks me - 'options for Loading all the projects within the components. Select how project folders are defined', But instead of clicking Next I just click Cancel. This shows my repository workspace as reachable and I am able to checkin the changes now.
But still the error is shown if I try to load the component from my repository workspace. Also note that there is no error if I try to load the whole repository workspace.

- Ankur

I have opened a workitem for this

https://jazz.net/jazz/web/projects/Rational%20Team%20Concert#action=com.ibm.team.workitem.viewWorkItem&id=71741

- Ankur