Needless to say, ~たことがあった is the past form of ~たことがある, so the reference point in time is past in the former, whereas it's now in the latter. The meaning is often the same, but not always so.
e.g.
遅刻したことがよくある。
遅刻したことがよくあった。
よくある means that the speaker is often late for school even now, but よくあった shows that it's past like "used to", i.e., it's not so now.
As for your example, the difference is subtle, but 見たことがあるのである has a nuance that 折紙 has just remembered her face now.