When was your continuation application filed, relative to the notice of appeal and the USPTO's panel decision? Without that information, it is impossible to determine whether an extension of time should have been paid to maintain copendency of the parent and the continuation.
Regardless, it is generally not possible to correct defects in a continuation filing by paying required extension of time fees late. This is why many firms maintain a deposit account and prophylactically authorize the USPTO to charge that deposit account for any required extensions of time, or any deficiency in an enclosed fee.
Why do we need the timing information noted above? Because the notice of appeal filed in support of the pre-appeal brief request for review tolls the response deadline to the last Office Action (i.e., the one prompting the Pre-Appeal). Thus, whether or not an extension of time was required to support the continuation filing will depend on when the notice of appeal was filed and when the panel decision was issued.
Per the OG notice regarding the pre-appeal brief conference program (available at
http://www.uspto.gov/web/offices/com/sol/og/2005/week28/patbref.htm)
"7. Time Periods Before/After a Panel Decision:
. The time period for filing an appeal brief will be reset to be one
month from mailing of the decision on the request, or the balance of
the two-month time period running from the receipt of the notice of
appeal, whichever is greater. Further, the time period for filing of
the appeal brief is extendible under 37 CFR 1.136 based upon the mail
date of the decision on the request or the receipt date of the notice
of appeal, as applicable. To the extent that any existing USPTO rule
is inconsistent with this pilot program, the rule is waived until
regulations directed to pre-appeal brief conferences are promulgated,
or the pilot program is ended. For example, if a request for a
pre-appeal brief conference is filed with a notice of appeal, the time
period set in 37 CFR 41.37(a)(1) is waived so that an appeal will not
stand dismissed if an appeal brief is not filed within two months of
the filing date of a notice of appeal, but is filed within one month
of the decision on the request."
I understand this to mean that if the continuation in your case was filed while the pre-appeal brief was pending, no EOT would be required. Similarly, I understand this to mean that if the continuation was filed witihn the window for filing an appeal brief after the panel decision, no EOT would be required. However, if the continuation was filed after the window for filing an appeal brief (or taking other action), an extension of time under 1.36 would be required.