Hi Bec,
This doesn't sound right to me. If your contract ended in September 2013, what contract have you been working under since then?
In the absence of a renewed contract, it is likely that a court would find that you have been working under an implied employment contract which may well be permanent full-time. In which case you shouldn't need to "re-apply" for your job.
For arguments sake, even if you did need to re-apply for your job, all your accrued benefits would still be available to you because you would be working continuously for the same employer. It's the same situation as if you applied for a promotion in your company. If you apply for the job, are offered and accept the job, all your employment benefits would still apply due to the continuous employment relationship.
I would appreciate it if you can provide some more information about your job and why your employer wants you to "re-apply".