Hi
I'm still not sure what the issue here is but I have used my Amigas on a home network consisting of a dozen PCs all hard wired through hubs and cables and they all have their shares set up on the Amiga and once logged in using NMBS and their specific SMBFS icon that I created their specific icon becomes available as a folder, and or complete drive to store Amiga files.
There are limitations on the file naming that is set out in the SMBFS guide and Windows restricts the use of certian file names. Over the last two days I have been backing up 2 SCSI drives and a 2.5" drive with 6GB of Amiga data using DOpus. I get one or two issues, but nothing serious. Within that are the current Workbench files of all the Amiga systems. There are only issues with |includes in AMOS, a " " file in MUI and the AUX file in Storage. Also CanDo has one or two example files that won't work and one of my animations is always flagged as busy. I've been backing up and using the PCs for decades now.
I also ZIP and CD copy using the Windows system.
Like I say, not sure whether this is a storage issue or whether you are trying to run programs from the PC side. That to me would be odd given that the Amiga is best at running Amiga programs. Never used an emulator or a Mac Linux etc system. Only use the Amigas and the PC. I also use a very slow system called AmiPC in times of urgent need. All have worked fine. I know what files have issues cus DOpus lets me know. I also have one XP machine set up as my hub or server for all my files which I drag Amiga programs and files off all the time across the network.
The SMBFS guide is very thorough on the various limitations. The program I assume has its limitations, but for me other than file names that the other OS doesn't allow I haven't ever experienced any loss of files and changes to files by the WindowsOS. I did get an odd problem with a file from one of the guides once that although found its way onto the Windows system could not be deleted.
Anyway, no doubt you are talking about something I know little of and I guess I kinda miss the point. It took me a long time to configure my SMB to get it all working properly on all the computers, but since I got it working has never failed. The reason I back up my Samba files and all the various Workbenches is that when I lose a hd I can quickly get back up and running. Fits on a ZIP and CD also so I have other options and even Parnet can get the ball rolling quickly. Networking is so important in keeping my gzillion computers fluid .... wouldn't be without all those wonderful cables. My internet is on a different network. Never cross the streams ... thats a rule not a guide , its the Venkman Rule. My A4000d 18GB is backed up regularly onto PC with no issue.... if I lost that it would be bad. I also only use conventional hard drives and trust me they all are fine. You have to hit the odd one with a hammer but they generally work fine.
This is a rather complicated matter to attend to. And i am no expert in the matter myself.
I just remember from the time i started using UAE and stored amiga files under windows managed folders that were mounted in uae as amiga drives. Having dynamic disk sizes was at times convenient.
But as time progressed executing files may cause strange behaviours both on amiga and pc side.
After asking about it here on this board i was promptly persuaded to start using hardfiles instead.
At the time being i was using windows XP
Long filenames and "." or "~" in filenames could at certain times cause malfunctions because windows interpreted the files differently form what the amiga was....
The same behavior could be experienced in using windows (NTFS or god forbid FAT) filesystems to store amiga files in a network.
If you however compress files before storing them the matter is irrelevant because the amiga file attributes or flags are maintained inside the compressed file.
As long as the compressing and uncompressing is happening inside the amiga environment.
What i want is an amiga native filesystem that operates as a file server in my network. completely independent from what my PCs do....
In addition i would have SMB mounted to pick up any media file i need on an amiga.
And i belive i have found a viable solution with NetFS and my Mac mini with MOS....

hope this clears up any misunderstanding, and if i am wrong at any point. please correct me.
If any one feel the need to elaborate even deeper, please feel free to do so.
I wonder at the matter myself, and to understand it better would be nice.
EDIT: Ooooh.. and a side note. Mounting ALL the windows drives as drives in the amiga (UAE) and use dopus 4.0 as a file manager to move or copy (maintain) files on the windows side is a really bad idea....... i have tried...... it worked GREAT for a time, then it suddenly just went awfully bad.... and i had to reformat two pc drives and lost bucket loads of data in the fall.... Highly NOT recommended.
And whether OP has found a solution to his query, i have absolutely no idea...