Yes, it can when your rate is one Soco can't see. Soco only knows the standard commission shown in TikTok Shop, so a deal you made privately with a brand looks like a standard-rate product to Add All to Showcase, and it can be replaced with the Soco link. For other products, Add All looks for a link with the same or higher commission than the rate Soco can see.
Rates Soco can't see
Both come down to your rate not being the standard TikTok Shop commission:
A private or direct brand deal: it never appears as the standard commission, so Soco can't compare against it.
A raise on a private rate, after you added the link: Soco checks rates only when you add a link, not continuously, so a later increase is invisible to it.
In these cases Soco sees only the standard rate and may replace your better link. Keep your own link on those products.
Protect a private rate
If you have one of these rates, don't use Add All: add your other links one by one.
Restore a link Add All already replaced
You can switch back right away. In TikTok, add the brand's own link to that product again: TikTok allows only one affiliate link per product, so your new link replaces the Soco link automatically. The step-by-step version, including what happens to videos you already posted: How do I switch a product back to a higher commission link?
Next steps
The wider mechanics: