How to deal with heterozygosity during polishing of genome assembly based on long reads?
A few possibilities:

Falcon

Try falcon and falcon-unzip. These are designed exactly for your problem and your data: https://github.com/PacificBiosciences/FALCON

Not Falcon

If you think you have assembled haplotypes (which seems reasonable to expect given enough coverage), you should be able to see the two haplotypes by just doing all pairwise alignments of your contigs. Haplotypes should show up as pairs of contigs that are MUCH more similar (even with a lot of between-haplotype divergence) than other pairs. Once you have all such pairs, you can simply select one of each pair to polish.