Flattening an image, changes it

When I flatten my image at completion, The images changes. Looks like my adjustment layers reset blending modes and adjustments. Tried uninstall, restart of photoshop and Mac, tried to flatten from tiff, psd and PDF. Same thing happens.. Please help!

Your layered and flattened documents are 16-bit RGB and the zoom is below 20%.
I bet the layered doc matches the flat one when they are viewed at 100% zoom.
Viewing at less than about 64% zoom when image Cache Levels is greater than 1 results in Photoshop taking shortcuts in calculating the display composite of a layered image, which will distort the appearance. Among the shortcuts is reduction of bit-depth from 16 to 8.
A flat document is, of course, not subject to display compositing shortcuts.
If you layer an image to achieve a particular look when zoomed to below 64% then it's likely to look significantly different when viewed at a greater zoom percentage, or when flattened.
Viewing at 100% is the only way to reliably determine the appearance of a document. Regardless of compositing distortion, the interpolation to produce Photoshop's zoomed-out display is not calculated in linear space (although it should be, in my opinion) so tones can be severely distorted, even in a flat document, at zoom less than 100%.
Something to try is going to Preferences > Performance and setting Cache Levels to 1 in order to avoid compositing shortcuts. However, Cache Levels 1 in combination with 16-bit mode can cause problems for some graphics cards. If you do change Cache Levels, relaunch Photoshop to ensure the change becomes effective.

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