The first time you updated the account number shouldn't count as an amendment as it's only a perfection given the FBAR wasn't accepted due to an illegal character in the first place.  The addition of the pension account should be the first amendment.  Even if one amendment had been filed, I don't see why PS would not allow another amendment to be submitted - I don't use PS, so can't comment on any peculiar restrictions PS may have imposed on the software though.

The alternative is to sign up for a BSA account and file it directly on their website.  There are pros and cons of going that route but that would always be one option if you have problems with filing using PS (or any other tax software).  You get instant validation before submission, so you won't have to wait a day or two before you know whether there are, for example, illegal characters that would need to be removed/changed.

Since you mention this is a pension account you were not aware of, you should also consider other implications as the plot gets a lot thicker with regard to potentially punitive tax regimes and other information return filing requirements which come with significant penalties, including the tolling of SOL.