Please disclose what kind parameters its updating in Context file and Env Files?
What is EBS version?
Custom top variable is being updated in Context file.
Old Value : <XX_TOP oa_var="s_xxtop" oa_type="PROD_TOP" oa_enabled="FALSE">/u01/app/ebs/apps/XX/12.0.0</XX_TOP>
New Value:<XX_TOP oa_var="s_xxtop" oa_type="PROD_TOP" oa_enabled="FALSE">/u01/app/ebs/apps/apps_st/appl/XX/12.0.0</XX_TOP>
EBS Version : 12.1.3.
Please take a look whether you have any duplicate entrees in table "FND_OAM_CONTEXT_files".
I don't see any duplicate entries.
For some reason some old vlaues or overwriting with intended values. Either you need to re-upload the existing context file.
Truncate this table "FND_OAM_CONTEXT_files" and re-run the autoconfig on all tiers.
Run FND_CONC_CLONE.SETUP_CLEAN and run autoconfig in all tiers including db Tier.
This is based on my experience, Just use it with your own risk
We tried this solution already but no luck.
Use adbldxml to recreate your context file, configure it, then run Autoconfig both tiers.
We have build context file with adbldxml only.