So I resolved the issue in this way:

1) Waited until the tx cleared from all mempools around the internet. blockcypher.com is handy for keeping track of that.
2) Now the tx is only in my local bitcoind's mempool. Stopped lightningd and bitcoind, deleted mempool.dat and restarted.
3) Issued "lightning-cli dev-rescan-outputs" command and now coins are back!