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You can apply for both, if applicable. First, your SSD will likely not be determine, yay or nay, for months. Then, unless it is fairly clear that you will meet the 12 month durational requirement of inability to work due to disability finding, you will likely be denied. You will then have to file your appeal within 60 days. If Reconsideration appeal is available, the same office that denied you will reconsider its decision and may deny again (statistically speaking, it most likely will). That will take another 2-3 to 4-8 months. Then you will have the opportunity to appeal to the real McCoy, an actual judge. The wait for his review and if needed, a hearing, is now generally between 1 and 3 years. Moreover, if and when you win SSD, the first 5 months are a "waiting period" and you are not entitled to disability benefits at all, so your start date of benefits would likely not coincide with receipt of any health benefits. Even if it did, it would not void SSD case or FMLA case retroactively.
So you see, if your disability doesn't extend beyond the 12 week max of FMLA, SSD will be denied anyway and if you go back to work with no problem, you would likely drop the SSD case to protect your rights later if you do actually become disabled for more than 12 months.
SSD should not void your FMLA, BUT, you by filing SSD, you are stating that you don't believe you will be able to work for at least 12 month, and if you return to work after 12 weeks or less of FMLA, and are able to so work, you will best be served by withdrawing your application for SSD.
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