Please show us an example of an offending upload_update and upload_insert script, and tell us how that script was created (MobilLink 16 Sybase Central wizard, or manual coding).
MobiLink has never used numbers to identify columns. Currently it uses names in MobiLink scripts by default, previously it used positional question marks "?" (and you can still use those but probably should not).
If tables have different column ordering on the consolidated and remote databases, it is a simple matter to code the MobiLink scripts to accomodate that difference. Manual coding is highly recommended. The wizard can be used but the resulting scripts must be checked for correctness because usage of the wizard is error prone even for small schema differences.
The bottom line: MobiLink scripts are entirely the responsibility of the developer.