How to activate the transparent table along with append structure

Hi,
I add the new fields in existing append structure on tale VBAP.
Initially i provide them the data type as Char with length 20.
Similarly i added the fields in user exit on scree 8459 to add fields on screen.
Until this eveything was working fine.
Then my functional consultant ask me to delete one field from structure and change the length of other data types to 40 characters.
I done this changes but when i go to activate that append structure its giving me error that certan structures in which it is been used are not adjusted and activated.
The table is not adjusted through SE14 - Database Utlity.
Its showing me that Runtime Object and Transparent table are different and not consistent.
Can i delete the runtime object?
The domains which i ave changed are also not geing activated.
Suggest me the node of problem and solution also.
What should be the problem.
What should i do to solve the problem.
Suggest me the solution if any.

Give a trail that instead of activating all together, activate low-level objects (domains, data elements etc)first and then high levels (structures, tables) individually. With this approach you could find the errors easily and can resolve quickly.
Regards,
Prasanth

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