The France U21 striker is set to join Premier League champions Liverpool in the coming days.
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Ekitike was missing for Saturday's friendly win against FSV Frankfurt with Toppmoller explaining afterwards: "He didn't play, but you can imagine everything else.
"This is a bitter loss.
"We lost our absolute top player in the winter with Omar Marmoush.
"The other player (Ekitike) stepped in and developed sensationally. It's quite possible that that's history, too.
"So I think we need to temper expectations a bit overall."