No, you do not reduce for losses. The PT rules require lost earnings even if there is a loss in the plan. You have to restore at least the fair market value of the use of the funds.
Rev. Ruling 2006-38 includes a discussion of the "amount involved". It references Temporary Reg. 141.4975-13, which says that Reg 53.4941(e)-1 controls for terms appearing in both 4941(e) and 4975(f). "Correction" appears in both those sections, too.
QUOTE
53.494-1(c)(4) Use of property by a disqualified person
(i) In the case of the use by a disqualified person of property owned by a private foundation, undoing the transaction includes, but is not limited to, terminating the use of such property. In addition to termination, the disqualified person must pay the foundation --
(a) The excess (if any) of the fair market value of the use of the property over the amount paid by the disqualified person for such use until such termination, and
(b) The excess (if any) of the amount which would have been paid by the disqualified person for the use of the property on or after the date of such termination, for the period such disqualified person would have used the property (without regard to any further extensions or renewals of such period) if such termination had not occurred, over the fair market value of such use for such period.
In applying (a) of this subdivision the fair market value of the use of property shall be the higher of the rate (that is, fair rental value per period in the case of use of property other than money or fair interest rate in the case of use of money) at the time of the act of self-dealing (within the meaning of paragraph (e)(1) of this section) or such rate at the time of correction of such act of self-dealing. In applying (b) of this subdivision the fair market value of the use of property shall be the rate at the time of correction.