Flow watermarking is an efficient technique for linking packet flows that helps thwart various attacks in networks such as over the Internet. Current state-of-the-art water-marking schemes withstand packet losses at the expense of compromising invisibility. We present an invisible flow watermarking scheme that can endure large numbers of packet losses. To maintain invisibility, our scheme embeds quantization-index modulation watermarks into inter-packet delays (as opposed to intervals). As the watermark is injected within individual packets, packet losses may lead to water-mark desynchronization and substitution errors. To deal with this issue we propose a maximum likelihood decoding (ML) scheme based on a hidden-Markov model (HMM) of the channel. Experimental results demonstrate that our scheme is robust to both network jitters and packet deletions while remaining invisible to an attacker.