When you find some skills and endorsements missing on your LinkedIn profile then these may be the reasons behind it:
You can have only 50 skills in your profile and if you want to add more then remove some skills to add.
In case you have removed some skills before to add more then the endorsements attached to those skills would also be removed. So, you would have to re-add a skill that was removed.
Type the skill exactly as it was displayed before on your profile. Only then you would get the previous endorsements back.
The endorsements attached to the skill would reappear only after you re-add the skill.
In case your endorsement is missing then it means the person who endorsed you would have removed their endorsement. But due to member privacy, LinkedIn will not be able to to tell you if the member choose to remove the endorsements.
In case you broke connection with another member or that person broke the connection then any endorsements between two of you would be removed automatically. Even if you re-establish the connection the endorsement would not be reinstated.