Hello Karel Grulich,
This issue is not related to Windows for Business or Windows 365 Enterprise. It is specifically a Windows Server integrity and servicing problem.
The behavior you describe that sfc /scannow detecting corruption, DISM /restorehealth repairing it, and then corruption reappearing after reboot indicates that the underlying problem is not simply missing system files but a recurring corruption caused either by a faulty driver, third‑party software, or disk integrity issues. When corruption returns after every restart, it usually points to one of three root causes:
Underlying storage problems: If the system volume has bad sectors or failing hardware, repaired files will be corrupted again on reboot. Running chkdsk /f /r on the system drive and reviewing the event logs under Event Viewer > Windows Logs > System for disk errors is critical.
Malware or third‑party filter drivers: Certain antivirus or endpoint protection agents inject DLLs or replace system binaries. After DISM repairs them, the agent reverts them back. You can check C:\Windows\Logs\CBS\CBS.log after each sfc run to see which files are repeatedly flagged. If the same files are always corrupted, that points to a specific driver or agent.
Servicing stack or image mismatch: If the install.wim you are using as the source does not match the exact build and cumulative update level of the server, DISM repairs will succeed temporarily but Windows File Protection will overwrite them again on reboot. You need to ensure the WIM source is from the same build as the server (winver to confirm). If the server is patched beyond the WIM image, use /source:WIM:<path> from updated installation media or /source:ESD from the latest ISO.
The best practice here is to first confirm disk health, then isolate which files are being corrupted repeatedly by reviewing CBS.log. If it is always the same set of files, you need to identify the driver or agent causing it. If it is widespread, the system image may be unrecoverable, in which case an in‑place upgrade repair using the latest Windows Server 2025 ISO is the supported fix.
If none of these steps resolve the issue, and corruption keeps returning after every reboot, it is likely a deeper servicing stack bug. In that case, the only compliant path is to open a case with Microsoft Support and wait for an official fix, since repeated manual repairs will not hold.
I hope you've found something useful here. If it helps you get more insight into the issue, it's appreciated to accept the answer. Should you have more questions, feel free to leave a message. Have a nice day!
Domic Vo.