Can airlines prevent me from flying in this complex situation?

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Time spent in the Schengen area in the last 180 days as of last week of the visa : Less than 2 months.

Irrelevant in the case of a D visa/Residence Permit, as stays in the issuing country are not counted against the Schengen clock

This means border agents of Schengen area might not see my residence application on their system because the system relies on the data Portugal enters

Until the EES (Entry Exit System) is rolled out later this year or next year, there are no global systems for those purposes.

A non-Portuguese border guard will only rely on what you actually present physically, be it a residence permit, a visa, etc. A Portuguese one may check in some databases for the Residence Permit, but this is not widespread

Direct flights to PT are quite rare.

If this is a possibility, you can transit through Turkey, the UK or the middle-eastern states, they all have direct flights to Lisbon or Porto and have (all but the UK) very lax visa requirements for transit.

can the airline create problems

Of course, they can, but wrongful, denial of boarding, i.e. you did have the correct paperwork, but they still deny you boarding, is, if you are taking an EU airline (Turkish and Emirates for example are out of the question, even though the Turkish civil aviation authority has a similar policy), very expensive for the airline in compensation (EU261, up to €600), so they better not deny you for invalid reasons

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