Here is a workaround for this on Ubuntu 20.04, which I suspect will work everywhere.
As other people have found, the problem is that the inodes for files in shared directories are wildly unstable. It turns out that there's a manual page for mount.prl_fs, which tells you about an option called host_inodes, which appears to make the inode numbers stable (it passes through inode numbers from the underlying filesystem).
So, then I spent some time working out how the tools actually mount things, and, at least on Ubuntu this is, thankfully, not via some systemd horror, but by a little daemon which is /usr/bin/prlfsmountd. And that's a shell script! So you can edit it - it already uses host_inodes for home directories, but you can just force it to use this option everywhere. Below is a diff, but you can just add it by hand to MNT_OPS in the script. I then bounced the VM and it's fine (I didn't bother working out how to restart it all with the VM up).
With luck this will make it into a patch release: it looks like a small problem for once.
---cut for diff, I hope this does not get mangled---
--- prlfsmountd.20200830 2020-08-11 13:43:45.218411070 +0100
+++ prlfsmountd 2020-08-30 12:52:45.112938240 +0100
@@ -9,7 +9,7 @@
MOUNTS=/etc/mtab
SF_LIST=/proc/fs/prl_fs/sf_list
POLL_TIME=5
-MNT_OPS=sync,nosuid,nodev,noatime,share
+MNT_OPS=sync,nosuid,nodev,noatime,share,host_inodes
# In addition to MNT_OPS for the Home folder
MNT_OPS_HOME=host_inodes
PRL_LOG=/var/log/parallels.log