The sign in front of the Church of the Redeemer, which features the message "All are welcome," was split in half.
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Church officials say they put up the flags every year for Pride month, but put them up a few days early in memory of a lesbian member whose funeral was taking place at the church.
"That's what hurt especially, I had seen it before the funeral," said Rev. Cynthia Black. "Word got around during the funeral and at a time that was already hard, to have to see that was just heartbreaking."
The church is proud of where the congregation stands when it comes to displaying support for Pride.
The church has been the target of hate before on its smaller signs.
"Someone took a bat to it or something to that, and when we replaced it we bought two because we fully expected it would happen again," Black said. "We just never imagined that this kind of thing would happen."
The Episcopal church is looking for donations to help fund the replacement of the sign, which they say cost $15,000 to put up in 2015.
"Even if we can't afford to replace it, we'll keep welcoming everyone," church officials said in a statement.
The Morris County Prosecutor's Office and Morristown police are investigating the vandalism.
Click here to visit the church's website to help.
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