If you are not changing anything on the array and are not doing anything with VMFS partitions on LUNs you should be on safe side.
Even if host detects a permanent device loss and then at some point re-discovers the SCSI device, if there is a VMFS partition detected there, host will try to mount and use it without changing any metadata, unless you request to do so.
After zone change and re-scan the host should detect the paths and configure multipathing automatically.
Dangerous things that can cause data loss and should be avoided:
- deleting the datastore from host
- changing LUN properties on array or deleting the LUN on array
- changing LUN presentation on array
- changing datastore properties from host (i.e. resignaturing)
And another thought - if you're having just 2 hosts, multiple initiator zoning should not cause you too much trouble. Main reason why VMware recommends SIZoning is that the RSCN/LIP event (someone enters or leaves the fabric, i.e. host is being shut down or booted up) might temporarily freeze I/O for other initiators within the same zone. If you're not rebooting your hosts every day, that should rarely be the case even with multi initiator zoning. If you are going to have more hosts in nearest future, then building it up correctly from very beginning is not a bad idea.
I might not know all the details of your environment but from what you've shared the zone config change sounds fairly simple and safe. However storage operations are always risky because things can be messed up very quickly. If you're not a storage / ESXi / FC expert, check if you can get one to hold your hand or even do this for you. If you're having just 2 hosts then whole procedure should not take more than 20 minutes (including time you spend searching for your FC switch password 
)
WBR
Imants