@Daniel Bulakh, Thanks for posting in Q&A. From your description, the win32 app shows installed without installing the new version on the device which is with previous version. Based on my experience, the issue can be with the detection rule. In fact, detection rule is used to detect if the app is installed on the device. If the detection rule we configure also satisfy the previous version, then it will consider the app is already installed and not do next.
https://learn.microsoft.com/en-us/mem/intune/apps/apps-win32-add#step-4-detection-rules
Please check on the detection rule and make sure the registry or file we configure is only for the new version. If there's any update, feel free to let us know.
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