The Hungarian’s contract with the Cottagers is set to expire this summer.
Gera was sent-off against Arsenal on Sunday for a lunge on Thomas Vermaelen.
“We were desperately disappointed for Zoltan,” Hughes told Sky Sports.
“I’m still hopeful that he’s going to stay next year but he’s got options and he’s keeping them open and he’s within his rights to do that.”
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Chelsea have struggled to build momentum in the opening stages of the campaign and are currently looking over their shoulders at the relegation zone.
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