When you install the 386 HPFS option, it installs a device driver that automatically initiates the HPFS partition on which you are installing, to 386 HPFS. The data integrity remains the same (a format is not required if the partition or drive is already formatted HPFS).
With OS/2 LAN Server 3.0 Advanced, HPFS drives (other than the install drive) do not become 386 HPFS drives until the OS/2 LAN Server 3.0 Advanced code uses/touches that drive. For example, the HPFS drive will remain simple HFPS until an alias, a NET SHARE, or access control profile is created on that drive. Therefore, a particular partition may not be a 386 HPFS drive unless you have used that drive in association with OS/2 LAN Server 3.0 Advanced.
To "make" an existing drive a 386 HPFS drive, try creating an alias for a resource on it. If this does not resolve the situation, try running CHKDSK with the /F parameter on that drive.
Note that if you need to keep certain partitions FAT or simple HPFS it is important to not have OS/2 LAN Server 3.0 Advanced deal with that particular partition (which you are using for another file system). If the 3.0 system does use that partition it will become 386 HPFS "formatted" and the other file system will not be able to utilize that drive again.